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Manganese in PDB 7jrq: Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein

Protein crystallography data

The structure of Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein, PDB code: 7jrq was solved by S.I.Mann, W.F.Degrado, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.68 / 1.75
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 45.322, 45.322, 164.22, 90, 90, 90
R / Rfree (%) 19.5 / 23

Other elements in 7jrq:

The structure of Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein (pdb code 7jrq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein, PDB code: 7jrq:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 7jrq

Go back to Manganese Binding Sites List in 7jrq
Manganese binding site 1 out of 2 in the Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:19.4
occ:1.00
MN1 A:SMU202 0.0 19.4 1.0
N3 A:SMU202 2.0 19.1 1.0
N2 A:SMU202 2.0 20.9 1.0
N1 A:SMU202 2.1 18.9 1.0
N4 A:SMU202 2.1 13.9 1.0
NE2 A:HIS64 2.4 17.0 1.0
O A:HOH322 2.6 22.7 1.0
C11 A:SMU202 3.0 15.8 1.0
C9 A:SMU202 3.0 19.4 1.0
C6 A:SMU202 3.1 18.9 1.0
C14 A:SMU202 3.1 18.3 1.0
C19 A:SMU202 3.1 17.5 1.0
C4 A:SMU202 3.1 20.5 1.0
C16 A:SMU202 3.1 17.8 1.0
C1 A:SMU202 3.1 19.8 1.0
CD2 A:HIS64 3.3 15.8 1.0
C10 A:SMU202 3.4 19.4 1.0
CE1 A:HIS64 3.4 18.6 1.0
C5 A:SMU202 3.5 17.5 1.0
C20 A:SMU202 3.5 20.8 1.0
C15 A:SMU202 3.5 18.5 1.0
C8 A:SMU202 4.3 23.5 1.0
C7 A:SMU202 4.3 21.3 1.0
C12 A:SMU202 4.3 20.0 1.0
C13 A:SMU202 4.3 19.8 1.0
C18 A:SMU202 4.3 18.6 1.0
C17 A:SMU202 4.4 19.8 1.0
C3 A:SMU202 4.4 18.8 1.0
C2 A:SMU202 4.4 20.5 1.0
O A:HOH326 4.5 23.6 1.0
CG A:HIS64 4.5 16.6 1.0
ND1 A:HIS64 4.5 15.6 1.0
O A:ALA121 4.8 22.5 1.0
C21 A:SMU202 5.0 18.8 1.0
C27 A:SMU202 5.0 24.2 1.0
CA A:GLY125 5.0 23.0 1.0

Manganese binding site 2 out of 2 in 7jrq

Go back to Manganese Binding Sites List in 7jrq
Manganese binding site 2 out of 2 in the Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn203

b:24.5
occ:0.52
MN1 A:SMU203 0.0 24.5 0.5
N2 A:SMU203 1.9 20.4 0.5
N1 A:SMU203 2.0 20.2 0.5
N3 A:SMU203 2.1 21.0 0.5
N4 A:SMU203 2.2 19.7 0.5
OE1 A:GLU58 2.6 24.6 1.0
C6 A:SMU203 3.0 21.3 0.5
C4 A:SMU203 3.0 20.1 0.5
C9 A:SMU203 3.0 20.3 0.5
C1 A:SMU203 3.1 21.5 0.5
C11 A:SMU203 3.1 19.9 0.5
C19 A:SMU203 3.2 21.0 0.5
C14 A:SMU203 3.2 19.1 0.5
C16 A:SMU203 3.2 21.3 0.5
CD A:GLU58 3.3 21.4 0.6
C5 A:SMU203 3.3 21.6 0.5
C10 A:SMU203 3.4 18.6 0.5
C20 A:SMU203 3.5 21.7 0.5
OE2 A:GLU58 3.5 27.1 1.0
C15 A:SMU203 3.6 19.1 0.5
NH2 A:ARG96 4.2 20.9 1.0
C7 A:SMU203 4.2 18.9 0.5
C8 A:SMU203 4.2 21.1 0.5
C3 A:SMU203 4.2 23.5 0.5
C2 A:SMU203 4.3 18.2 0.5
NE A:ARG96 4.3 18.9 1.0
C12 A:SMU203 4.4 20.2 0.5
C13 A:SMU203 4.4 18.5 0.5
C18 A:SMU203 4.4 22.7 0.5
C17 A:SMU203 4.5 21.5 0.5
CG A:GLU58 4.5 25.9 1.0
CB A:GLU58 4.6 22.4 1.0
CZ A:ARG96 4.6 24.8 1.0
C21 A:SMU203 4.8 20.9 0.5

Reference:

S.I.Mann, A.Nayak, G.T.Gassner, M.J.Therien, W.F.Degrado. De Novo Design, Solution Characterization, and Crystallographic Structure of An Abiological Mn-Porphyrin-Binding Protein Capable of Stabilizing A Mn(V) Species. J.Am.Chem.Soc. 2020.
ISSN: ESSN 1520-5126
PubMed: 33373215
DOI: 10.1021/JACS.0C10136
Page generated: Sun Oct 6 08:48:31 2024

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