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Zinc in PDB 4n7l: Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides

Protein crystallography data

The structure of Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides, PDB code: 4n7l was solved by A.Hardjasa, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.57 / 2.85
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 139.590, 139.590, 184.052, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 21.6

Other elements in 4n7l:

The structure of Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides also contains other interesting chemical elements:

Iron (Fe) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides (pdb code 4n7l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides, PDB code: 4n7l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4n7l

Go back to Zinc Binding Sites List in 4n7l
Zinc binding site 1 out of 6 in the Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn305

b:43.6
occ:1.00
ZN L:2GO305 0.0 43.6 1.0
ND L:2GO305 2.0 47.1 1.0
NC L:2GO305 2.0 51.3 1.0
NA L:2GO305 2.0 47.2 1.0
NB L:2GO305 2.0 44.6 1.0
NE2 L:HIS173 2.2 29.9 1.0
C4D L:2GO305 2.9 47.8 1.0
OBB M:2GO404 2.9 54.2 1.0
C1A L:2GO305 3.0 45.0 1.0
C1C L:2GO305 3.0 47.9 1.0
C4C L:2GO305 3.0 45.2 1.0
C4A L:2GO305 3.0 40.6 1.0
C1B L:2GO305 3.0 44.9 1.0
C4B L:2GO305 3.1 43.6 1.0
CE1 L:HIS173 3.1 32.6 1.0
C1D L:2GO305 3.1 46.1 1.0
CD2 L:HIS173 3.3 33.5 1.0
CHC L:2GO305 3.4 45.0 1.0
CHA L:2GO305 3.4 47.4 1.0
CHB L:2GO305 3.4 37.9 1.0
CHD L:2GO305 3.5 44.2 1.0
CAB M:2GO404 3.5 55.5 1.0
CBB M:2GO404 4.1 57.0 1.0
C3D L:2GO305 4.2 47.9 1.0
ND1 L:HIS173 4.2 32.6 1.0
C3A L:2GO305 4.3 42.5 1.0
C2A L:2GO305 4.3 43.7 1.0
C2D L:2GO305 4.3 48.0 1.0
C3C L:2GO305 4.3 42.5 1.0
C3B L:2GO305 4.3 47.4 1.0
C2C L:2GO305 4.4 41.5 1.0
CG L:HIS173 4.4 34.0 1.0
C2B L:2GO305 4.4 47.1 1.0
C3B M:2GO404 4.4 53.8 1.0
CD1 L:PHE167 4.7 50.0 1.0
CMA L:2GO305 4.9 45.6 1.0
CBD L:2GO305 4.9 46.2 1.0

Zinc binding site 2 out of 6 in 4n7l

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Zinc binding site 2 out of 6 in the Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn311

b:0.4
occ:1.00
ZN L:2GO311 0.0 0.4 1.0
NA L:2GO311 2.0 1.0 1.0
ND L:2GO311 2.1 0.2 1.0
NC L:2GO311 2.1 0.2 1.0
NB L:2GO311 2.1 0.9 1.0
C4D L:2GO311 3.0 0.8 1.0
C4A L:2GO311 3.0 0.6 1.0
C1A L:2GO311 3.0 0.1 1.0
C1C L:2GO311 3.1 0.5 1.0
C4C L:2GO311 3.1 0.9 1.0
C4B L:2GO311 3.1 0.2 1.0
C1B L:2GO311 3.1 0.8 1.0
C1D L:2GO311 3.2 0.6 1.0
CHC L:2GO311 3.4 0.2 1.0
CHB L:2GO311 3.4 1.0 1.0
CHA L:2GO311 3.5 0.9 1.0
CHD L:2GO311 3.6 0.2 1.0
CD1 L:LEU185 3.9 52.9 1.0
CB M:ALA153 4.2 38.6 1.0
CD2 L:LEU185 4.2 51.0 1.0
C3D L:2GO311 4.2 98.5 1.0
C3A L:2GO311 4.4 0.8 1.0
C2A L:2GO311 4.4 0.9 1.0
C3B L:2GO311 4.4 1.0 1.0
C2C L:2GO311 4.4 92.5 1.0
C2D L:2GO311 4.4 99.9 1.0
C3C L:2GO311 4.4 91.2 1.0
C2B L:2GO311 4.5 0.1 1.0
C7 M:2GO404 4.5 54.8 1.0
CG L:LEU185 4.5 50.5 1.0
CB L:LEU185 4.6 47.3 1.0
CE1 M:PHE150 4.7 49.7 1.0
C10 M:2GO404 4.7 57.9 1.0
CD1 M:PHE150 4.8 49.3 1.0
CBD L:2GO311 4.9 88.0 1.0

Zinc binding site 3 out of 6 in 4n7l

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Zinc binding site 3 out of 6 in the Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn401

b:37.0
occ:1.00
ZN M:2GO401 0.0 37.0 1.0
NC M:2GO401 2.0 31.8 1.0
NA M:2GO401 2.0 31.2 1.0
NB M:2GO401 2.0 32.9 1.0
ND M:2GO401 2.0 29.6 1.0
NE2 L:HIS153 2.5 44.8 1.0
C4D M:2GO401 2.9 28.8 1.0
C1C M:2GO401 2.9 38.7 1.0
C4C M:2GO401 2.9 33.3 1.0
C1A M:2GO401 3.0 31.6 1.0
C4A M:2GO401 3.0 31.2 1.0
C1B M:2GO401 3.0 32.6 1.0
C4B M:2GO401 3.0 36.2 1.0
C1D M:2GO401 3.1 32.0 1.0
CD2 L:HIS153 3.2 47.3 1.0
CHA M:2GO401 3.4 28.6 1.0
CHC M:2GO401 3.4 36.4 1.0
CHB M:2GO401 3.4 30.2 1.0
CHD M:2GO401 3.5 32.6 1.0
CE1 L:HIS153 3.5 50.1 1.0
C3D M:2GO401 4.2 31.0 1.0
C3C M:2GO401 4.3 37.7 1.0
C2C M:2GO401 4.3 40.6 1.0
C3A M:2GO401 4.3 31.4 1.0
C2A M:2GO401 4.3 34.0 1.0
C3B M:2GO401 4.3 38.7 1.0
C2B M:2GO401 4.3 34.8 1.0
C2D M:2GO401 4.4 32.5 1.0
CG L:HIS153 4.5 51.1 1.0
CE2 M:TYR210 4.6 42.6 1.0
ND1 L:HIS153 4.6 53.1 1.0
OBB M:2GO402 4.6 53.1 1.0
CBD M:2GO401 4.8 33.0 1.0
CBA M:2GO401 4.9 44.1 1.0
C20 M:2GO402 4.9 45.0 1.0
CD1 L:LEU154 4.9 44.2 1.0

Zinc binding site 4 out of 6 in 4n7l

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Zinc binding site 4 out of 6 in the Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn402

b:42.9
occ:1.00
ZN M:2GO402 0.0 42.9 1.0
NA M:2GO402 2.0 46.0 1.0
NB M:2GO402 2.0 41.1 1.0
NC M:2GO402 2.0 42.1 1.0
ND M:2GO402 2.0 39.8 1.0
ND1 M:HIS214 2.3 37.2 1.0
C4D M:2GO402 2.9 41.7 1.0
CE1 M:HIS214 3.0 39.5 1.0
C1A M:2GO402 3.0 44.0 1.0
C4A M:2GO402 3.0 42.0 1.0
C1B M:2GO402 3.0 42.2 1.0
C1C M:2GO402 3.0 40.2 1.0
C4C M:2GO402 3.0 38.9 1.0
C4B M:2GO402 3.1 39.5 1.0
C1D M:2GO402 3.1 37.1 1.0
CHB M:2GO402 3.3 44.5 1.0
CHA M:2GO402 3.4 40.3 1.0
CHC M:2GO402 3.4 36.2 1.0
CHD M:2GO402 3.5 36.3 1.0
CG M:HIS214 3.5 42.0 1.0
CB M:HIS214 4.1 41.8 1.0
C3D M:2GO402 4.2 41.6 1.0
NE2 M:HIS214 4.2 43.4 1.0
C2A M:2GO402 4.3 42.6 1.0
C3B M:2GO402 4.3 41.2 1.0
C3A M:2GO402 4.3 38.3 1.0
C2B M:2GO402 4.3 41.7 1.0
C2C M:2GO402 4.4 41.4 1.0
C2D M:2GO402 4.4 40.7 1.0
C3C M:2GO402 4.4 37.3 1.0
CD2 M:HIS214 4.5 41.3 1.0
CB L:ALA124 4.5 43.2 1.0
CA M:HIS214 4.7 41.5 1.0
CE1 L:PHE121 4.8 41.7 1.0
CBD M:2GO402 4.9 41.2 1.0
CD1 L:PHE121 4.9 41.8 1.0

Zinc binding site 5 out of 6 in 4n7l

Go back to Zinc Binding Sites List in 4n7l
Zinc binding site 5 out of 6 in the Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn403

b:38.5
occ:1.00
ZN M:2GO403 0.0 38.5 1.0
NA M:2GO403 2.0 37.4 1.0
ND M:2GO403 2.0 33.7 1.0
NC M:2GO403 2.0 37.1 1.0
NB M:2GO403 2.0 36.2 1.0
NE2 M:HIS182 2.3 44.4 1.0
C4D M:2GO403 2.9 34.6 1.0
C1A M:2GO403 2.9 39.2 1.0
C4A M:2GO403 3.0 37.6 1.0
C1B M:2GO403 3.0 37.9 1.0
C1C M:2GO403 3.0 37.8 1.0
C4C M:2GO403 3.0 35.0 1.0
C4B M:2GO403 3.1 35.2 1.0
C1D M:2GO403 3.1 33.8 1.0
CE1 M:HIS182 3.2 44.3 1.0
CD2 M:HIS182 3.3 44.6 1.0
CHA M:2GO403 3.3 36.4 1.0
CHB M:2GO403 3.4 37.8 1.0
CHC M:2GO403 3.4 37.5 1.0
CHD M:2GO403 3.5 33.6 1.0
C3D M:2GO403 4.1 37.3 1.0
C3A M:2GO403 4.2 37.5 1.0
C2A M:2GO403 4.3 41.9 1.0
C2B M:2GO403 4.3 39.4 1.0
C2D M:2GO403 4.3 37.2 1.0
C3C M:2GO403 4.3 36.1 1.0
C3B M:2GO403 4.3 39.4 1.0
ND1 M:HIS182 4.3 45.0 1.0
C2C M:2GO403 4.4 37.1 1.0
CG M:HIS182 4.4 44.8 1.0
OBB L:2GO311 4.7 75.1 1.0
CE2 L:PHE181 4.8 44.6 1.0
CBD M:2GO403 4.8 37.7 1.0
CMA M:2GO403 4.9 38.2 1.0

Zinc binding site 6 out of 6 in 4n7l

Go back to Zinc Binding Sites List in 4n7l
Zinc binding site 6 out of 6 in the Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn404

b:42.5
occ:1.00
ZN M:2GO404 0.0 42.5 1.0
NC M:2GO404 2.0 48.4 1.0
ND M:2GO404 2.0 41.7 1.0
NA M:2GO404 2.0 50.5 1.0
NB M:2GO404 2.0 47.1 1.0
NE2 M:HIS202 2.2 31.3 1.0
C4C M:2GO404 3.0 44.0 1.0
C4D M:2GO404 3.0 40.7 1.0
C4A M:2GO404 3.0 49.1 1.0
C1C M:2GO404 3.0 50.3 1.0
C1B M:2GO404 3.0 49.3 1.0
C1A M:2GO404 3.0 46.0 1.0
C4B M:2GO404 3.1 48.4 1.0
C1D M:2GO404 3.1 41.9 1.0
CE1 M:HIS202 3.2 33.9 1.0
CD2 M:HIS202 3.2 35.4 1.0
CHB M:2GO404 3.3 49.1 1.0
CHC M:2GO404 3.4 49.7 1.0
CHA M:2GO404 3.4 42.6 1.0
CHD M:2GO404 3.5 44.2 1.0
CBB L:2GO305 3.5 50.5 1.0
CAB L:2GO305 3.7 46.0 1.0
OBB L:2GO305 3.8 41.3 1.0
C3D M:2GO404 4.2 39.9 1.0
C3C M:2GO404 4.3 45.4 1.0
ND1 M:HIS202 4.3 32.6 1.0
C2C M:2GO404 4.3 47.0 1.0
C2D M:2GO404 4.3 40.5 1.0
C3A M:2GO404 4.3 47.8 1.0
CG M:HIS202 4.3 32.8 1.0
C2B M:2GO404 4.3 51.4 1.0
C3B M:2GO404 4.4 53.8 1.0
C2A M:2GO404 4.4 46.7 1.0
C3B L:2GO305 4.5 47.4 1.0
CBD M:2GO404 4.9 41.8 1.0
CAC M:2GO404 5.0 45.3 1.0

Reference:

R.G.Saer, J.Pan, A.Hardjasa, S.Lin, F.Rosell, A.G.Mauk, N.W.Woodbury, M.E.Murphy, J.T.Beatty. Structural and Kinetic Properties of Rhodobacter Sphaeroides Photosynthetic Reaction Centers Containing Exclusively Zn-Coordinated Bacteriochlorophyll As Bacteriochlorin Cofactors. Biochim.Biophys.Acta V.1837 366 2014.
ISSN: ISSN 0006-3002
PubMed: 24316146
DOI: 10.1016/J.BBABIO.2013.11.015
Page generated: Wed Dec 16 05:36:38 2020

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