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Magnesium in PDB 6ae9: X-Ray Structure of the Photosystem II Phosphatase Pbcp

Enzymatic activity of X-Ray Structure of the Photosystem II Phosphatase Pbcp

All present enzymatic activity of X-Ray Structure of the Photosystem II Phosphatase Pbcp:
3.1.3.16;

Protein crystallography data

The structure of X-Ray Structure of the Photosystem II Phosphatase Pbcp, PDB code: 6ae9 was solved by X.Y.Liu, J.C.Chai, X.M.Ou, Z.F.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.70 / 1.47
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 166.407, 166.407, 46.983, 90.00, 90.00, 120.00
R / Rfree (%) 16 / 17.9

Other elements in 6ae9:

The structure of X-Ray Structure of the Photosystem II Phosphatase Pbcp also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of the Photosystem II Phosphatase Pbcp (pdb code 6ae9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the X-Ray Structure of the Photosystem II Phosphatase Pbcp, PDB code: 6ae9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6ae9

Go back to Magnesium Binding Sites List in 6ae9
Magnesium binding site 1 out of 6 in the X-Ray Structure of the Photosystem II Phosphatase Pbcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of the Photosystem II Phosphatase Pbcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:12.7
occ:1.00
 OD1 A:ASP79 2.0 13.8 1.0
O A:GLY80 2.0 15.3 1.0
O A:HOH521 2.0 14.3 1.0
O A:HOH538 2.0 15.8 1.0
O4 A:PO4404 2.1 14.1 1.0
O1 A:PO4404 2.4 14.1 1.0
P A:PO4404 2.8 14.3 1.0
CG A:ASP79 3.1 11.9 1.0
C A:GLY80 3.2 14.7 1.0
OD2 A:ASP79 3.7 12.6 1.0
MN A:MN406 3.8 13.7 0.7
O A:HOH579 3.8 16.0 1.0
O A:HOH630 3.8 15.1 1.0
N A:GLY80 3.9 12.5 1.0
O3 A:PO4404 3.9 16.2 1.0
O2 A:PO4404 3.9 15.7 1.0
N A:SER82 4.0 18.5 1.0
OG A:SER82 4.0 20.4 1.0
C A:ASP79 4.0 10.8 1.0
CA A:GLY80 4.1 13.0 1.0
OD1 A:ASP63 4.1 14.3 1.0
N A:VAL81 4.1 13.7 1.0
CA A:VAL81 4.2 15.3 1.0
OD2 A:ASP284 4.2 16.0 1.0
O A:HOH525 4.3 14.4 1.0
C A:VAL81 4.4 19.2 1.0
CB A:ASP79 4.4 12.4 1.0
O A:ASP79 4.4 11.9 1.0
CB A:GLU62 4.4 18.6 1.0
CA A:ASP79 4.5 12.1 1.0
OE1 A:GLU62 4.5 29.3 1.0
O A:GLU62 4.7 15.1 1.0
C A:GLU62 4.8 14.6 1.0
CA A:SER82 4.9 17.8 1.0
CB A:SER82 4.9 20.9 1.0
NZ A:LYS56 5.0 32.6 1.0
OD1 A:ASN283 5.0 16.6 1.0

Magnesium binding site 2 out of 6 in 6ae9

Go back to Magnesium Binding Sites List in 6ae9
Magnesium binding site 2 out of 6 in the X-Ray Structure of the Photosystem II Phosphatase Pbcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of the Photosystem II Phosphatase Pbcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:13.6
occ:1.00
 O2 A:PO4404 2.0 15.7 1.0
OD2 A:ASP210 2.1 16.9 1.0
O A:HOH541 2.1 15.1 1.0
O A:HOH596 2.1 18.8 1.0
O A:HOH613 2.1 16.5 1.0
O A:HOH546 2.1 15.2 1.0
CG A:ASP210 3.1 14.7 1.0
P A:PO4404 3.3 14.3 1.0
OD1 A:ASP210 3.4 14.0 1.0
MN A:MN406 3.7 13.7 0.7
O1 A:PO4404 3.8 14.1 1.0
O A:HOH630 3.9 15.1 1.0
O3 A:PO4404 3.9 16.2 1.0
OD2 A:ASP152 3.9 16.3 1.0
OD1 A:ASP175 4.0 20.4 1.0
NZ A:LYS281 4.0 22.7 1.0
O A:HOH562 4.1 31.7 1.0
OD1 A:ASP152 4.2 13.2 1.0
OD2 A:ASP79 4.3 12.6 1.0
O A:HOH608 4.4 22.4 1.0
CB A:ASP210 4.4 13.2 1.0
O4 A:PO4404 4.4 14.1 1.0
CG A:ASP152 4.5 15.0 1.0
O A:HOH576 4.5 23.1 1.0
CE A:LYS281 4.7 42.6 1.0
O A:HOH616 4.8 13.8 1.0
CG A:PRO177 4.9 15.3 1.0
OD1 A:ASN283 4.9 16.6 1.0
ND2 A:ASN283 5.0 16.7 1.0
CG A:ASP175 5.0 22.4 1.0

Magnesium binding site 3 out of 6 in 6ae9

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Magnesium binding site 3 out of 6 in the X-Ray Structure of the Photosystem II Phosphatase Pbcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of the Photosystem II Phosphatase Pbcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:22.5
occ:1.00
 O A:HOH560 2.0 21.8 1.0
O A:HOH741 2.1 27.8 1.0
O A:HOH641 2.1 27.1 1.0
O A:HOH528 2.1 24.9 1.0
O A:HOH576 2.1 23.1 1.0
O A:HOH549 2.1 23.6 1.0
OE1 A:GLU171 3.9 21.9 1.0
OD2 A:ASP152 3.9 16.3 1.0
O A:HOH623 3.9 36.1 1.0
OD1 A:ASP214 4.0 23.2 1.0
OE1 A:GLU258 4.2 29.9 1.0
O A:HOH557 4.2 33.1 1.0
OD2 A:ASP214 4.2 19.4 1.0
OD1 A:ASP175 4.3 20.4 1.0
OE2 A:GLU258 4.4 35.4 1.0
CG A:ASP214 4.5 17.8 1.0
CD A:GLU258 4.6 35.8 1.0
O A:HOH546 4.6 15.2 1.0
N A:ASP175 4.7 19.6 1.0
CA A:ASP175 4.7 18.6 1.0
CG A:ASP152 4.7 15.0 1.0
CB A:ASP152 4.8 12.7 1.0
CE1 A:PHE174 4.8 21.3 1.0
CD1 A:TYR255 4.9 21.7 1.0
CD A:GLU171 4.9 26.9 1.0

Magnesium binding site 4 out of 6 in 6ae9

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Magnesium binding site 4 out of 6 in the X-Ray Structure of the Photosystem II Phosphatase Pbcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Structure of the Photosystem II Phosphatase Pbcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:10.8
occ:1.00
 O B:GLY80 2.0 12.1 1.0
OD1 B:ASP79 2.0 11.4 1.0
O B:HOH563 2.0 12.2 1.0
O B:HOH553 2.1 12.3 1.0
O2 B:PO4404 2.1 12.5 1.0
O4 B:PO4404 2.4 12.1 1.0
P B:PO4404 2.8 12.4 1.0
CG B:ASP79 3.2 9.6 1.0
C B:GLY80 3.2 12.3 1.0
OD2 B:ASP79 3.7 11.0 1.0
O B:HOH566 3.8 13.5 1.0
MN B:MN407 3.8 11.4 0.7
O3 B:PO4404 3.9 14.2 1.0
N B:GLY80 3.9 11.0 1.0
O B:HOH675 3.9 12.1 1.0
O1 B:PO4404 3.9 12.4 1.0
C B:ASP79 4.0 10.3 1.0
OG B:SER82 4.0 16.0 1.0
CA B:GLY80 4.1 11.4 1.0
N B:SER82 4.1 13.6 1.0
OD1 B:ASP63 4.1 11.5 1.0
N B:VAL81 4.1 12.6 1.0
CA B:VAL81 4.2 12.3 1.0
OD2 B:ASP284 4.3 13.5 1.0
O B:HOH550 4.3 11.8 1.0
O B:ASP79 4.4 10.6 1.0
CB B:GLU62 4.4 13.6 1.0
CB B:ASP79 4.4 10.0 1.0
C B:VAL81 4.4 13.9 1.0
OE1 B:GLU62 4.4 23.6 1.0
CA B:ASP79 4.5 11.4 1.0
NZ B:LYS56 4.6 16.6 0.5
O B:GLU62 4.7 12.8 1.0
CA B:SER82 4.8 15.5 1.0
C B:GLU62 4.8 12.6 1.0
CB B:SER82 4.9 14.0 1.0

Magnesium binding site 5 out of 6 in 6ae9

Go back to Magnesium Binding Sites List in 6ae9
Magnesium binding site 5 out of 6 in the X-Ray Structure of the Photosystem II Phosphatase Pbcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Structure of the Photosystem II Phosphatase Pbcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:11.2
occ:1.00
 O1 B:PO4404 2.1 12.4 1.0
O B:HOH574 2.1 11.7 1.0
O B:HOH552 2.1 13.8 1.0
OD2 B:ASP210 2.1 13.3 1.0
O B:HOH649 2.1 15.1 1.0
O B:HOH581 2.2 17.3 1.0
CG B:ASP210 3.1 12.9 1.0
P B:PO4404 3.3 12.4 1.0
OD1 B:ASP210 3.5 10.9 1.0
MN B:MN407 3.7 11.4 0.7
O4 B:PO4404 3.8 12.1 1.0
OD2 B:ASP152 3.9 14.3 1.0
O3 B:PO4404 3.9 14.2 1.0
O B:HOH675 4.0 12.1 1.0
OD1 B:ASP175 4.0 17.8 1.0
NZ B:LYS281 4.0 20.9 1.0
O B:HOH517 4.1 29.1 1.0
OD1 B:ASP152 4.2 11.1 1.0
OD2 B:ASP79 4.3 11.0 1.0
O B:HOH605 4.4 19.6 1.0
CB B:ASP210 4.4 9.8 1.0
CG B:ASP152 4.5 12.6 1.0
O2 B:PO4404 4.5 12.5 1.0
O B:HOH556 4.5 18.3 1.0
OD1 B:ASN283 4.8 15.4 1.0
O B:HOH637 4.8 12.6 1.0
CG B:ASP175 4.8 19.7 1.0
CG B:PRO177 4.9 12.8 1.0

Magnesium binding site 6 out of 6 in 6ae9

Go back to Magnesium Binding Sites List in 6ae9
Magnesium binding site 6 out of 6 in the X-Ray Structure of the Photosystem II Phosphatase Pbcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of X-Ray Structure of the Photosystem II Phosphatase Pbcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:19.2
occ:1.00
 O B:HOH540 2.0 18.8 1.0
O B:HOH547 2.1 19.8 1.0
O B:HOH763 2.1 22.3 1.0
O B:HOH628 2.1 21.4 1.0
O B:HOH546 2.1 20.2 1.0
O B:HOH556 2.1 18.3 1.0
OD2 B:ASP152 3.9 14.3 1.0
OE1 B:GLU171 3.9 22.6 1.0
OD1 B:ASP214 4.0 18.8 1.0
O B:HOH607 4.1 26.0 1.0
O B:HOH516 4.1 29.5 1.0
OE1 B:GLU258 4.2 25.5 1.0
OD1 B:ASP175 4.2 17.8 1.0
OD2 B:ASP214 4.2 16.4 1.0
OE2 B:GLU258 4.3 30.0 1.0
CG B:ASP214 4.5 15.7 1.0
CD B:GLU258 4.6 27.0 1.0
CA B:ASP175 4.7 15.2 1.0
O B:HOH552 4.7 13.8 1.0
N B:ASP175 4.7 16.5 1.0
CG B:ASP152 4.7 12.6 1.0
CB B:ASP152 4.8 11.7 1.0
CE1 B:PHE174 4.9 20.4 1.0
CD B:GLU171 4.9 24.9 1.0

Reference:

X.Liu, J.Chai, X.Ou, M.Li, Z.Liu. Structural Insights Into Substrate Selectivity, Catalytic Mechanism, and Redox Regulation of Rice Photosystem II Core Phosphatase. Mol Plant V. 12 86 2019.
ISSN: ESSN 1752-9867
PubMed: 30453087
DOI: 10.1016/J.MOLP.2018.11.006
Page generated: Mon Sep 30 19:05:56 2024

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