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Zinc in PDB 4rlr: Structure of Monoheme Cytochrome Pcch From Geobacter Sulfurreducens

Protein crystallography data

The structure of Structure of Monoheme Cytochrome Pcch From Geobacter Sulfurreducens, PDB code: 4rlr was solved by P.R.Pokkuluri, C.A.Salgueiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.55 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 63.311, 63.311, 78.682, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.2

Other elements in 4rlr:

The structure of Structure of Monoheme Cytochrome Pcch From Geobacter Sulfurreducens also contains other interesting chemical elements:

Arsenic (As) 1 atom
Iron (Fe) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Monoheme Cytochrome Pcch From Geobacter Sulfurreducens (pdb code 4rlr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Monoheme Cytochrome Pcch From Geobacter Sulfurreducens, PDB code: 4rlr:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4rlr

Go back to Zinc Binding Sites List in 4rlr
Zinc binding site 1 out of 3 in the Structure of Monoheme Cytochrome Pcch From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Monoheme Cytochrome Pcch From Geobacter Sulfurreducens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:32.0
occ:1.00
O1A A:HEM201 1.9 21.3 1.0
OD2 A:ASP62 2.0 29.1 1.0
O A:HOH449 2.0 29.3 1.0
O A:HOH301 2.1 24.7 1.0
OD1 A:ASP62 2.4 25.6 1.0
CG A:ASP62 2.5 27.9 1.0
CGA A:HEM201 2.9 22.6 1.0
O2A A:HEM201 3.3 20.0 1.0
CB A:ALA65 3.6 24.8 1.0
O A:HOH345 3.9 31.1 1.0
CB A:ASP62 4.0 24.7 1.0
CBA A:HEM201 4.3 19.1 1.0
NH2 A:ARG68 4.4 25.5 1.0
OH A:TYR29 4.6 40.2 1.0
CE1 A:TYR29 4.6 30.9 1.0
CZ A:TYR29 4.7 36.4 1.0
CA A:ALA65 4.9 21.9 1.0
CD1 A:TYR57 4.9 17.5 1.0
CAA A:HEM201 4.9 20.9 1.0
CE1 A:TYR57 5.0 20.5 1.0

Zinc binding site 2 out of 3 in 4rlr

Go back to Zinc Binding Sites List in 4rlr
Zinc binding site 2 out of 3 in the Structure of Monoheme Cytochrome Pcch From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Monoheme Cytochrome Pcch From Geobacter Sulfurreducens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:42.6
occ:1.00
O2 A:CAC205 1.8 46.0 1.0
NE2 A:HIS30 2.0 31.8 1.0
O A:HOH316 2.1 31.6 1.0
CE1 A:HIS30 2.9 27.6 1.0
CD2 A:HIS30 3.0 27.5 1.0
AS A:CAC205 3.3 98.9 1.0
C2 A:CAC205 3.8 43.4 1.0
O A:HOH309 3.8 34.2 1.0
ND1 A:HIS30 4.0 28.7 1.0
CG A:HIS30 4.1 26.2 1.0
O1 A:CAC205 4.3 54.5 1.0
C1 A:CAC205 4.6 41.3 1.0
CD2 A:TYR29 4.6 30.1 1.0
CE2 A:TYR29 4.7 34.2 1.0

Zinc binding site 3 out of 3 in 4rlr

Go back to Zinc Binding Sites List in 4rlr
Zinc binding site 3 out of 3 in the Structure of Monoheme Cytochrome Pcch From Geobacter Sulfurreducens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Monoheme Cytochrome Pcch From Geobacter Sulfurreducens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:23.0
occ:1.00
O A:ACT206 1.9 23.2 1.0
ND1 A:HIS87 2.1 21.3 1.0
O A:HOH346 2.1 23.0 1.0
CE1 A:HIS87 2.9 24.3 1.0
C A:ACT206 2.9 25.4 1.0
CG A:HIS87 3.1 20.8 1.0
OXT A:ACT206 3.2 26.1 1.0
CB A:HIS87 3.6 21.7 1.0
CA A:HIS87 3.7 21.8 1.0
CMC A:HEM201 3.7 22.8 1.0
NE2 A:HIS87 4.1 22.3 1.0
O A:HOH383 4.1 30.7 1.0
CD2 A:HIS87 4.2 20.9 1.0
O A:HOH362 4.3 25.1 1.0
CH3 A:ACT206 4.3 27.0 1.0
O A:ARG16 4.3 19.8 1.0
O A:HIS87 4.4 21.4 1.0
C A:HIS87 4.6 22.5 1.0
N A:HIS87 4.6 23.1 1.0
O A:ARG86 5.0 24.8 1.0
C2C A:HEM201 5.0 19.8 1.0

Reference:

J.M.Dantas, L.M.Campelo, N.E.Duke, C.A.Salgueiro, P.R.Pokkuluri. The Structure of Pcch From Geobacter Sulfurreducens: A Novel Low Reduction Potential Monoheme Cytochrome Essential For Accepting Electrons From An Electrode. Febs J. 2015.
ISSN: ISSN 1742-464X
PubMed: 25786707
DOI: 10.1111/FEBS.13269
Page generated: Wed Dec 16 05:45:57 2020

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