eF-site ID 6w1q-d
PDB Code 6w1q
Chain d

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Title RT XFEL structure of Photosystem II 50 microseconds after the second illumination at 2.27 Angstrom resolution
Classification PHOTOSYNTHESIS
Compound Photosystem II protein D1 1
Source ORGANISM_SCIENTIFIC: Thermosynechococcus elongatus (strain BP-1);
Sequence d:  RGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTG
TTFVTSWYTHGLASSYLEGCNFLTVAVSTPANSMGHSLLL
LWGPEAQGDFTRWCQLGGLWTFIALHGAFGLIGFMLRQFE
IARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAP
SFGVAAIFRFLLFFQGFHNWTLNPFHMMGVAGVLGGALLC
AIHGATVENTLFQDGEGASTFRAFNPTQAEETYSMVTANR
FWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLAL
NLRSYDFISQEIRAAEDPEFETFYTKNLLLNEGIRAWMAP
QDQPHENFVFPEEVLPRGNAL
Description


Functional site

1) chain d
residue 214
type
sequence H
description binding site for residue FE2 a 401
source : AM7

2) chain d
residue 268
type
sequence H
description binding site for residue FE2 a 401
source : AM7

3) chain d
residue 205
type
sequence L
description binding site for residue CLA a 402
source : AM8

4) chain d
residue 157
type
sequence F
description binding site for residue CLA a 403
source : AM9

5) chain d
residue 175
type
sequence V
description binding site for residue CLA a 403
source : AM9

6) chain d
residue 178
type
sequence I
description binding site for residue CLA a 403
source : AM9

7) chain d
residue 179
type
sequence F
description binding site for residue CLA a 403
source : AM9

8) chain d
residue 182
type
sequence L
description binding site for residue CLA a 403
source : AM9

9) chain d
residue 205
type
sequence L
description binding site for residue PHO a 404
source : AN1

10) chain d
residue 208
type
sequence A
description binding site for residue PHO a 404
source : AN1

11) chain d
residue 209
type
sequence L
description binding site for residue PHO a 404
source : AN1

12) chain d
residue 213
type
sequence I
description binding site for residue PHO a 404
source : AN1

13) chain d
residue 253
type
sequence W
description binding site for residue PHO a 404
source : AN1

14) chain d
residue 257
type
sequence F
description binding site for residue PHO a 404
source : AN1

15) chain d
residue 317
type
sequence K
description binding site for residue CL a 407
source : AN4

16) chain d
residue 30
type
sequence V
description binding site for residue PL9 a 409
source : AN6

17) chain d
residue 39
type
sequence P
description binding site for residue PL9 a 409
source : AN6

18) chain d
residue 42
type
sequence Y
description binding site for residue PL9 a 409
source : AN6

19) chain d
residue 45
type
sequence L
description binding site for residue PL9 a 409
source : AN6

20) chain d
residue 230
type
sequence S
description binding site for residue SQD a 410
source : AN7

21) chain d
residue 233
type
sequence R
description binding site for residue SQD a 410
source : AN7

22) chain d
residue 27
type
sequence F
description binding site for residue LHG a 411
source : AN8

23) chain d
residue 159
type
sequence I
description binding site for residue CLA b 602
source : AO5

24) chain d
residue 196
type
sequence F
description binding site for residue CLA b 607
source : AP1

25) chain d
residue 281
type
sequence M
description binding site for residue CLA b 607
source : AP1

26) chain d
residue 120
type
sequence F
description binding site for residue CLA b 608
source : AP2

27) chain d
residue 123
type
sequence I
description binding site for residue CLA b 608
source : AP2

28) chain d
residue 126
type
sequence M
description binding site for residue CLA b 608
source : AP2

29) chain d
residue 139
type
sequence R
description binding site for residue LHG b 623
source : AQ8

30) chain d
residue 141
type
sequence Y
description binding site for residue LHG b 623
source : AQ8

31) chain d
residue 269
type
sequence F
description binding site for residue LHG b 623
source : AQ8

32) chain d
residue 276
type
sequence V
description binding site for residue LHG b 623
source : AQ8

33) chain d
residue 277
type
sequence T
description binding site for residue LHG b 623
source : AQ8

34) chain d
residue 16
type
sequence D
description binding site for residue STE b 629
source : AR5

35) chain d
residue 19
type
sequence D
description binding site for residue STE b 629
source : AR5

36) chain d
residue 23
type
sequence K
description binding site for residue STE b 629
source : AR5

37) chain d
residue 32
type
sequence W
description binding site for residue STE b 629
source : AR5

38) chain d
residue 41
type
sequence A
description binding site for residue PHO d 401
source : AT9

39) chain d
residue 48
type
sequence W
description binding site for residue PHO d 401
source : AT9

40) chain d
residue 114
type
sequence I
description binding site for residue PHO d 401
source : AT9

41) chain d
residue 121
type
sequence G
description binding site for residue PHO d 401
source : AT9

42) chain d
residue 122
type
sequence L
description binding site for residue PHO d 401
source : AT9

43) chain d
residue 125
type
sequence F
description binding site for residue PHO d 401
source : AT9

44) chain d
residue 129
type
sequence Q
description binding site for residue PHO d 401
source : AT9

45) chain d
residue 142
type
sequence N
description binding site for residue PHO d 401
source : AT9

46) chain d
residue 146
type
sequence F
description binding site for residue PHO d 401
source : AT9

47) chain d
residue 214
type
sequence H
description binding site for residue BCT d 402
source : AU1

48) chain d
residue 244
type
sequence Y
description binding site for residue BCT d 402
source : AU1

49) chain d
residue 264
type
sequence K
description binding site for residue BCT d 402
source : AU1

50) chain d
residue 268
type
sequence H
description binding site for residue BCT d 402
source : AU1

51) chain d
residue 149
type
sequence P
description binding site for residue CLA d 403
source : AU2

52) chain d
residue 152
type
sequence V
description binding site for residue CLA d 403
source : AU2

53) chain d
residue 156
type
sequence V
description binding site for residue CLA d 403
source : AU2

54) chain d
residue 181
type
sequence F
description binding site for residue CLA d 403
source : AU2

55) chain d
residue 182
type
sequence L
description binding site for residue CLA d 403
source : AU2

56) chain d
residue 185
type
sequence F
description binding site for residue CLA d 403
source : AU2

57) chain d
residue 191
type
sequence W
description binding site for residue CLA d 403
source : AU2

58) chain d
residue 192
type
sequence T
description binding site for residue CLA d 403
source : AU2

59) chain d
residue 197
type
sequence H
description binding site for residue CLA d 403
source : AU2

60) chain d
residue 200
type
sequence G
description binding site for residue CLA d 403
source : AU2

61) chain d
residue 201
type
sequence V
description binding site for residue CLA d 403
source : AU2

62) chain d
residue 282
type
sequence S
description binding site for residue CLA d 403
source : AU2

63) chain d
residue 283
type
sequence A
description binding site for residue CLA d 403
source : AU2

64) chain d
residue 286
type
sequence V
description binding site for residue CLA d 403
source : AU2

65) chain d
residue 198
type
sequence M
description binding site for residue CLA d 404
source : AU3

66) chain d
residue 201
type
sequence V
description binding site for residue CLA d 404
source : AU3

67) chain d
residue 202
type
sequence A
description binding site for residue CLA d 404
source : AU3

68) chain d
residue 35
type
sequence I
description binding site for residue CLA d 405
source : AU4

69) chain d
residue 40
type
sequence C
description binding site for residue CLA d 405
source : AU4

70) chain d
residue 43
type
sequence L
description binding site for residue CLA d 405
source : AU4

71) chain d
residue 89
type
sequence L
description binding site for residue CLA d 405
source : AU4

72) chain d
residue 90
type
sequence L
description binding site for residue CLA d 405
source : AU4

73) chain d
residue 91
type
sequence L
description binding site for residue CLA d 405
source : AU4

74) chain d
residue 92
type
sequence L
description binding site for residue CLA d 405
source : AU4

75) chain d
residue 93
type
sequence W
description binding site for residue CLA d 405
source : AU4

76) chain d
residue 112
type
sequence T
description binding site for residue CLA d 405
source : AU4

77) chain d
residue 113
type
sequence F
description binding site for residue CLA d 405
source : AU4

78) chain d
residue 116
type
sequence L
description binding site for residue CLA d 405
source : AU4

79) chain d
residue 117
type
sequence H
description binding site for residue CLA d 405
source : AU4

80) chain d
residue 42
type
sequence Y
description binding site for residue BCR d 406
source : AU5

81) chain d
residue 46
type
sequence G
description binding site for residue BCR d 406
source : AU5

82) chain d
residue 47
type
sequence G
description binding site for residue BCR d 406
source : AU5

83) chain d
residue 49
type
sequence L
description binding site for residue BCR d 406
source : AU5

84) chain d
residue 50
type
sequence T
description binding site for residue BCR d 406
source : AU5

85) chain d
residue 199
type
sequence M
description binding site for residue PL9 d 407
source : AU6

86) chain d
residue 214
type
sequence H
description binding site for residue PL9 d 407
source : AU6

87) chain d
residue 217
type
sequence T
description binding site for residue PL9 d 407
source : AU6

88) chain d
residue 253
type
sequence W
description binding site for residue PL9 d 407
source : AU6

89) chain d
residue 260
type
sequence A
description binding site for residue PL9 d 407
source : AU6

90) chain d
residue 261
type
sequence F
description binding site for residue PL9 d 407
source : AU6

91) chain d
residue 267
type
sequence L
description binding site for residue PL9 d 407
source : AU6

92) chain d
residue 257
type
sequence F
description binding site for residue LHG d 408
source : AU7

93) chain d
residue 260
type
sequence A
description binding site for residue LHG d 408
source : AU7

94) chain d
residue 261
type
sequence F
description binding site for residue LHG d 408
source : AU7

95) chain d
residue 262
type
sequence S
description binding site for residue LHG d 408
source : AU7

96) chain d
residue 263
type
sequence N
description binding site for residue LHG d 408
source : AU7

97) chain d
residue 266
type
sequence W
description binding site for residue LHG d 408
source : AU7

98) chain d
residue 219
type
sequence E
description binding site for residue LHG d 409
source : AU8

99) chain d
residue 220
type
sequence N
description binding site for residue LHG d 409
source : AU8

100) chain d
residue 229
type
sequence A
description binding site for residue LHG d 409
source : AU8

101) chain d
residue 231
type
sequence T
description binding site for residue LHG d 409
source : AU8

102) chain d
residue 232
type
sequence F
description binding site for residue LHG d 409
source : AU8

103) chain d
residue 67
type
sequence Y
description binding site for residue LMG d 410
source : AU9

104) chain d
residue 70
type
sequence G
description binding site for residue LMG d 410
source : AU9

105) chain d
residue 71
type
sequence C
description binding site for residue LMG d 410
source : AU9

106) chain d
residue 72
type
sequence N
description binding site for residue LMG d 410
source : AU9

107) chain d
residue 73
type
sequence F
description binding site for residue LMG d 410
source : AU9

108) chain d
residue 32
type
sequence W
description binding site for residue STE d 411
source : AV1

109) chain d
residue 134
type
sequence R
description binding site for residue STE d 411
source : AV1

110) chain d
residue 24
type
sequence R
description binding site for residue SQD f 102
source : AV3

111) chain d
residue 26
type
sequence R
description binding site for residue SQD f 102
source : AV3

112) chain d
residue 87
type
sequence H
description binding site for residue DGD h 101
source : AV4

113) chain d
residue 162
type
sequence L
description binding site for residue DGD h 101
source : AV4

114) chain d
residue 291
type
sequence L
description binding site for residue DGD h 101
source : AV4

115) chain d
residue 266
type
sequence W
description binding site for residue LHG l 101
source : AW1

116) chain d
residue 270
type
sequence F
description binding site for residue LHG l 101
source : AW1

117) chain d
residue 273
type
sequence F
description binding site for residue LHG l 101
source : AW1

118) chain d
residue 93
type
sequence W
description binding site for residue STE x 102
source : AW8

119) chain d
residue 300
type
sequence S
description binding site for Di-peptide FME m 1 and GLU m 2
source : AX1

120) chain d
residue 303
type
sequence I
description binding site for Di-peptide FME m 1 and GLU m 2
source : AX1

121) chain d
residue 304
type
sequence R
description binding site for Di-peptide FME m 1 and GLU m 2
source : AX1

122) chain d
residue 132-140
type TOPO_DOM
sequence IARLVGVRP
description Lumenal
source Swiss-Prot : SWS_FT_FI1

123) chain d
residue 218-265
type TOPO_DOM
sequence VENTLFQDGEGASTFRAFNPTQAEETYSMVTANRFWSQIF
GIAFSNKR
description Lumenal
source Swiss-Prot : SWS_FT_FI1

124) chain d
residue 268
type BINDING
sequence H
description BINDING => ECO:0000255|HAMAP-Rule:MF_01383, ECO:0000269|PubMed:16355230, ECO:0000269|PubMed:19219048, ECO:0000303|PubMed:14764885, ECO:0000303|PubMed:20558739, ECO:0000303|PubMed:21367867, ECO:0000303|PubMed:22665786, ECO:0000303|PubMed:23413188, ECO:0000303|PubMed:25006873, ECO:0000303|PubMed:25043005, ECO:0000303|DOI:10.1039/B406989G
source Swiss-Prot : SWS_FT_FI10

125) chain d
residue 266-288
type TRANSMEM
sequence WLHFFMLFVPVTGLWMSAIGVVG
description Helical => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI2

126) chain d
residue 32-53
type TRANSMEM
sequence WSGILLFPCAYLALGGWLTGTT
description Helical => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI2

127) chain d
residue 109-131
type TRANSMEM
sequence GLWTFIALHGAFGLIGFMLRQFE
description Helical => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI2

128) chain d
residue 141-160
type TRANSMEM
sequence YNAIAFSAPIAVFVSVFLIY
description Helical => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI2

129) chain d
residue 194-217
type TRANSMEM
sequence NPFHMMGVAGVLGGALLCAIHGAT
description Helical => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI2

130) chain d
residue 54-108
type TOPO_DOM
sequence FVTSWYTHGLASSYLEGCNFLTVAVSTPANSMGHSLLLLW
GPEAQGDFTRWCQLG
description Cytoplasmic => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI3

131) chain d
residue 161-193
type TOPO_DOM
sequence PLGQSSWFFAPSFGVAAIFRFLLFFQGFHNWTL
description Cytoplasmic => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI3

132) chain d
residue 289-352
type TOPO_DOM
sequence LALNLRSYDFISQEIRAAEDPEFETFYTKNLLLNEGIRAW
MAPQDQPHENFVFPEEVLPRGNAL
description Cytoplasmic => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI3

133) chain d
residue 142
type BINDING
sequence N
description BINDING => ECO:0000255|HAMAP-Rule:MF_01383, ECO:0000269|PubMed:16355230, ECO:0000269|PubMed:19219048, ECO:0000303|PubMed:20558739, ECO:0000303|PubMed:21367867, ECO:0000303|PubMed:25043005
source Swiss-Prot : SWS_FT_FI6

134) chain d
residue 197
type BINDING
sequence H
description axial binding residue => ECO:0000255|HAMAP-Rule:MF_01383, ECO:0000269|PubMed:16355230, ECO:0000269|PubMed:19219048, ECO:0000303|PubMed:14764885, ECO:0000303|PubMed:20558739, ECO:0000303|PubMed:21367867, ECO:0000303|PubMed:22665786, ECO:0000303|PubMed:23413188, ECO:0000303|PubMed:25043005, ECO:0000303|DOI:10.1039/B406989G
source Swiss-Prot : SWS_FT_FI7

135) chain d
residue 214
type BINDING
sequence H
description BINDING => ECO:0000255|HAMAP-Rule:MF_01383, ECO:0000269|PubMed:16355230, ECO:0000269|PubMed:19219048, ECO:0000303|PubMed:14764885, ECO:0000303|PubMed:20558739, ECO:0000303|PubMed:21367867, ECO:0000303|PubMed:22665786, ECO:0000303|PubMed:23413188, ECO:0000303|PubMed:25043005, ECO:0000303|DOI:10.1039/B406989G
source Swiss-Prot : SWS_FT_FI8

136) chain d
residue 261
type BINDING
sequence F
description BINDING => ECO:0000255|HAMAP-Rule:MF_01383, ECO:0000269|PubMed:16355230, ECO:0000269|PubMed:19219048, ECO:0000303|PubMed:14764885, ECO:0000303|PubMed:20558739, ECO:0000303|PubMed:21367867, ECO:0000303|PubMed:22665786, ECO:0000303|PubMed:23413188, ECO:0000303|PubMed:25006873, ECO:0000303|PubMed:25043005
source Swiss-Prot : SWS_FT_FI9


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