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Magnesium in PDB 7zyv: Cryo-Em Structure of Catalytically Active Spinacia Oleracea Cytochrome B6F in Complex with Endogenous Plastoquinones at 2.13 A Resolution

Enzymatic activity of Cryo-Em Structure of Catalytically Active Spinacia Oleracea Cytochrome B6F in Complex with Endogenous Plastoquinones at 2.13 A Resolution

All present enzymatic activity of Cryo-Em Structure of Catalytically Active Spinacia Oleracea Cytochrome B6F in Complex with Endogenous Plastoquinones at 2.13 A Resolution:
7.1.1.6;

Other elements in 7zyv:

The structure of Cryo-Em Structure of Catalytically Active Spinacia Oleracea Cytochrome B6F in Complex with Endogenous Plastoquinones at 2.13 A Resolution also contains other interesting chemical elements:

Iron (Fe) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Catalytically Active Spinacia Oleracea Cytochrome B6F in Complex with Endogenous Plastoquinones at 2.13 A Resolution (pdb code 7zyv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of Catalytically Active Spinacia Oleracea Cytochrome B6F in Complex with Endogenous Plastoquinones at 2.13 A Resolution, PDB code: 7zyv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7zyv

Go back to Magnesium Binding Sites List in 7zyv
Magnesium binding site 1 out of 2 in the Cryo-Em Structure of Catalytically Active Spinacia Oleracea Cytochrome B6F in Complex with Endogenous Plastoquinones at 2.13 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Catalytically Active Spinacia Oleracea Cytochrome B6F in Complex with Endogenous Plastoquinones at 2.13 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:72.3
occ:1.00
MG A:CLA304 0.0 72.3 1.0
NB A:CLA304 2.0 72.3 1.0
ND A:CLA304 2.0 72.3 1.0
NA A:CLA304 2.1 72.3 1.0
NC A:CLA304 2.1 72.3 1.0
C4D A:CLA304 2.9 72.3 1.0
C1B A:CLA304 3.0 72.3 1.0
HL3 B:UMQ403 3.0 79.3 1.0
C4A A:CLA304 3.1 72.3 1.0
C4B A:CLA304 3.1 72.3 1.0
C1C A:CLA304 3.1 72.3 1.0
C4C A:CLA304 3.1 72.3 1.0
C1A A:CLA304 3.1 72.3 1.0
C1D A:CLA304 3.2 72.3 1.0
CHB A:CLA304 3.4 72.3 1.0
CHC A:CLA304 3.4 72.3 1.0
CHA A:CLA304 3.5 72.3 1.0
CHD A:CLA304 3.5 72.3 1.0
HL2 B:UMQ403 3.7 79.3 1.0
CL B:UMQ403 3.9 79.3 1.0
HJ1 B:UMQ403 4.2 79.3 1.0
C3D A:CLA304 4.3 72.3 1.0
C2B A:CLA304 4.3 72.3 1.0
C3B A:CLA304 4.3 72.3 1.0
C2C A:CLA304 4.3 72.3 1.0
C2D A:CLA304 4.4 72.3 1.0
C3C A:CLA304 4.4 72.3 1.0
C3A A:CLA304 4.4 72.3 1.0
C2A A:CLA304 4.5 72.3 1.0
HL1 B:UMQ403 4.5 79.3 1.0
CK B:UMQ403 4.9 79.3 1.0
CBD A:CLA304 4.9 72.3 1.0

Magnesium binding site 2 out of 2 in 7zyv

Go back to Magnesium Binding Sites List in 7zyv
Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Catalytically Active Spinacia Oleracea Cytochrome B6F in Complex with Endogenous Plastoquinones at 2.13 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Catalytically Active Spinacia Oleracea Cytochrome B6F in Complex with Endogenous Plastoquinones at 2.13 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg304

b:72.4
occ:1.00
MG I:CLA304 0.0 72.4 1.0
NB I:CLA304 2.0 72.4 1.0
ND I:CLA304 2.0 72.4 1.0
NA I:CLA304 2.1 72.4 1.0
NC I:CLA304 2.1 72.4 1.0
C4D I:CLA304 2.9 72.4 1.0
C1B I:CLA304 3.0 72.4 1.0
C4A I:CLA304 3.1 72.4 1.0
C4B I:CLA304 3.1 72.4 1.0
C1C I:CLA304 3.1 72.4 1.0
HL3 J:UMQ404 3.1 78.9 1.0
C4C I:CLA304 3.1 72.4 1.0
C1A I:CLA304 3.1 72.4 1.0
C1D I:CLA304 3.2 72.4 1.0
CHB I:CLA304 3.4 72.4 1.0
CHC I:CLA304 3.4 72.4 1.0
CHA I:CLA304 3.5 72.4 1.0
CHD I:CLA304 3.5 72.4 1.0
HL2 J:UMQ404 3.7 78.9 1.0
CL J:UMQ404 3.9 78.9 1.0
HJ2 J:UMQ404 4.2 78.9 1.0
C3D I:CLA304 4.3 72.4 1.0
C2B I:CLA304 4.3 72.4 1.0
C3B I:CLA304 4.3 72.4 1.0
C2C I:CLA304 4.3 72.4 1.0
C2D I:CLA304 4.4 72.4 1.0
C3C I:CLA304 4.4 72.4 1.0
C3A I:CLA304 4.4 72.4 1.0
C2A I:CLA304 4.5 72.4 1.0
HL1 J:UMQ404 4.6 78.9 1.0
CK J:UMQ404 4.9 78.9 1.0
CBD I:CLA304 4.9 72.4 1.0

Reference:

M.Sarewicz, M.Szwalec, S.Pintscher, P.Indyka, M.Rawski, R.Pietras, B.Mielecki, L.Koziej, M.Jaciuk, S.Glatt, A.Osyczka. High-Resolution Cryo-Em Structures of Plant Cytochrome B 6 F at Work. Sci Adv V. 9 D9688 2023.
ISSN: ESSN 2375-2548
PubMed: 36638176
DOI: 10.1126/SCIADV.ADD9688
Page generated: Thu Oct 3 17:07:09 2024

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