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Manganese in PDB 9jet: Crystal Structure of A Cupin Protein (TM1459) in Manganese (Mn) Substituted Form

Protein crystallography data

The structure of Crystal Structure of A Cupin Protein (TM1459) in Manganese (Mn) Substituted Form, PDB code: 9jet was solved by N.Fujieda, H.Ichihashi, G.Kurisu, S.Itoh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.575, 57.863, 74.796, 90, 90, 90
R / Rfree (%) n/a / n/a

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of A Cupin Protein (TM1459) in Manganese (Mn) Substituted Form (pdb code 9jet). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of A Cupin Protein (TM1459) in Manganese (Mn) Substituted Form, PDB code: 9jet:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 9jet

Go back to Manganese Binding Sites List in 9jet
Manganese binding site 1 out of 2 in the Crystal Structure of A Cupin Protein (TM1459) in Manganese (Mn) Substituted Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of A Cupin Protein (TM1459) in Manganese (Mn) Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1201

b:14.8
occ:0.82
NE2 A:HIS58 2.1 17.4 1.0
NE2 A:HIS92 2.2 16.3 1.0
NE2 A:HIS54 2.2 15.7 1.0
NE2 A:HIS52 2.2 16.6 1.0
O A:HOH1382 2.3 22.4 1.0
O A:HOH1380 2.3 23.2 1.0
CE1 A:HIS92 3.0 13.9 1.0
CE1 A:HIS52 3.1 17.2 1.0
CD2 A:HIS58 3.1 19.3 1.0
CE1 A:HIS58 3.1 21.8 1.0
CE1 A:HIS54 3.1 14.9 1.0
HE1 A:HIS92 3.1 16.7 1.0
HE1 A:HIS52 3.2 20.6 1.0
HE1 A:HIS54 3.2 17.9 1.0
CD2 A:HIS92 3.2 14.8 1.0
CD2 A:HIS54 3.2 17.5 1.0
HD2 A:HIS58 3.3 23.2 1.0
HE1 A:HIS58 3.3 26.1 1.0
CD2 A:HIS52 3.3 16.4 1.0
HD2 A:HIS54 3.4 21.0 1.0
HD2 A:HIS92 3.5 17.7 1.0
HD2 A:HIS52 3.5 19.7 1.0
ND1 A:HIS92 4.2 13.3 1.0
ND1 A:HIS58 4.2 17.0 1.0
ND1 A:HIS52 4.2 16.1 1.0
CG A:HIS58 4.2 17.3 1.0
ND1 A:HIS54 4.3 15.8 1.0
CG A:HIS92 4.3 14.2 1.0
CG A:HIS52 4.4 14.9 1.0
CG A:HIS54 4.4 13.9 1.0
O A:HOH1387 4.4 17.7 1.0
O A:HOH1402 4.4 48.4 1.0
HE2 A:PHE94 4.5 21.9 1.0
HD1 A:HIS92 4.9 16.0 1.0
HD1 A:HIS52 5.0 19.3 1.0
HD1 A:HIS58 5.0 20.4 1.0

Manganese binding site 2 out of 2 in 9jet

Go back to Manganese Binding Sites List in 9jet
Manganese binding site 2 out of 2 in the Crystal Structure of A Cupin Protein (TM1459) in Manganese (Mn) Substituted Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of A Cupin Protein (TM1459) in Manganese (Mn) Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2201

b:14.9
occ:0.92
NE2 B:HIS58 2.1 16.6 1.0
NE2 B:HIS92 2.1 15.7 1.0
NE2 B:HIS52 2.2 16.2 1.0
NE2 B:HIS54 2.2 16.2 1.0
O B:HOH2391 2.3 22.7 1.0
O B:HOH2397 2.4 24.2 1.0
CE1 B:HIS92 3.0 13.7 1.0
CE1 B:HIS52 3.1 14.6 1.0
CE1 B:HIS54 3.1 17.9 1.0
CD2 B:HIS58 3.1 15.7 1.0
CE1 B:HIS58 3.1 19.7 1.0
HE1 B:HIS54 3.2 21.5 1.0
HE1 B:HIS92 3.2 16.5 1.0
HE1 B:HIS52 3.2 17.6 1.0
CD2 B:HIS52 3.2 17.9 1.0
CD2 B:HIS92 3.2 14.9 1.0
HD2 B:HIS58 3.3 18.9 1.0
HE1 B:HIS58 3.3 23.6 1.0
CD2 B:HIS54 3.3 17.3 1.0
HD2 B:HIS52 3.4 21.5 1.0
HD2 B:HIS92 3.4 17.8 1.0
HD2 B:HIS54 3.6 20.7 1.0
ND1 B:HIS92 4.2 12.9 1.0
ND1 B:HIS52 4.2 14.6 1.0
ND1 B:HIS58 4.2 19.4 1.0
CG B:HIS58 4.3 18.3 1.0
ND1 B:HIS54 4.3 18.6 1.0
CG B:HIS52 4.3 13.9 1.0
CG B:HIS92 4.3 13.0 1.0
O B:HOH2374 4.3 24.0 1.0
HE2 B:PHE94 4.3 16.5 1.0
CG B:HIS54 4.4 16.4 1.0
O B:HOH2434 4.8 55.5 1.0
HD1 B:HIS92 4.9 15.5 1.0
HD1 B:HIS52 5.0 17.6 1.0

Reference:

N.Fujieda, K.I.Ishihama, H.Ichihashi, S.Yanagisawa, G.Kurisu, S.Itoh. Unusual Self-Hydroxylation in 4-Histidine Tetrad-Supporting Nonheme Iron Center. Chem Asian J 01191 2025.
ISSN: ESSN 1861-471X
PubMed: 40260495
DOI: 10.1002/ASIA.202401191
Page generated: Sun Aug 17 02:37:31 2025

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