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Manganese in PDB 4rb3: Crystal Structure of Magnetospirillum Gryphiswaldense Msr-1 Fur-MN2+- FEOAB1 Operator

Protein crystallography data

The structure of Crystal Structure of Magnetospirillum Gryphiswaldense Msr-1 Fur-MN2+- FEOAB1 Operator, PDB code: 4rb3 was solved by Z.Deng, Z.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.56 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.995, 68.642, 83.995, 90.00, 108.70, 90.00
R / Rfree (%) 23.2 / 26.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Magnetospirillum Gryphiswaldense Msr-1 Fur-MN2+- FEOAB1 Operator (pdb code 4rb3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Magnetospirillum Gryphiswaldense Msr-1 Fur-MN2+- FEOAB1 Operator, PDB code: 4rb3:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4rb3

Go back to Manganese Binding Sites List in 4rb3
Manganese binding site 1 out of 4 in the Crystal Structure of Magnetospirillum Gryphiswaldense Msr-1 Fur-MN2+- FEOAB1 Operator


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 Magnetospirillum Gryphiswaldense Msr-1 Fur-MN2+- FEOAB1 Operator within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn200

b:54.8
occ:1.00
OE1 C:GLU108 2.0 60.3 1.0
O C:HOH306 2.0 36.8 1.0
NE2 C:HIS125 2.1 55.2 1.0
NE2 C:HIS87 2.2 59.1 1.0
OD2 C:ASP89 2.4 58.1 1.0
OD1 C:ASP89 2.5 58.9 1.0
CG C:ASP89 2.7 59.8 1.0
CE1 C:HIS125 2.8 56.6 1.0
CD C:GLU108 2.9 62.3 1.0
OE2 C:GLU108 3.1 62.3 1.0
CE1 C:HIS87 3.1 60.1 1.0
CD2 C:HIS87 3.2 63.8 1.0
CD2 C:HIS125 3.3 56.8 1.0
ND1 C:HIS125 4.0 56.3 1.0
CB C:ASP89 4.2 59.4 1.0
ND1 C:HIS87 4.3 62.8 1.0
CG C:HIS125 4.3 58.0 1.0
CG C:GLU108 4.3 65.8 1.0
CG C:HIS87 4.3 65.2 1.0
NE2 C:GLN111 4.4 56.8 1.0
O C:HOH303 4.5 38.2 1.0
OE1 C:GLN111 4.6 57.5 1.0
N C:ASP89 4.8 60.5 1.0
CA C:ASP89 4.9 58.9 1.0
CD C:GLN111 4.9 57.6 1.0
CB C:LEU127 4.9 53.1 1.0
C C:HIS88 4.9 63.1 1.0

Manganese binding site 2 out of 4 in 4rb3

Go back to Manganese Binding Sites List in 4rb3
Manganese binding site 2 out of 4 in the Crystal Structure of Magnetospirillum Gryphiswaldense Msr-1 Fur-MN2+- FEOAB1 Operator


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 Magnetospirillum Gryphiswaldense Msr-1 Fur-MN2+- FEOAB1 Operator within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn201

b:60.2
occ:1.00
NE2 C:HIS88 2.2 66.4 1.0
OE2 C:GLU101 2.3 65.4 1.0
NE2 C:HIS90 2.3 51.4 1.0
OE2 C:GLU81 2.3 56.8 1.0
OE1 C:GLU81 2.4 55.1 1.0
NE2 C:HIS33 2.4 63.4 1.0
CD C:GLU81 2.7 57.0 1.0
CD C:GLU101 3.0 63.4 1.0
CE1 C:HIS90 3.1 52.0 1.0
CE1 C:HIS88 3.1 67.1 1.0
CD2 C:HIS88 3.2 67.6 1.0
CD2 C:HIS33 3.4 64.1 1.0
CD2 C:HIS90 3.4 51.2 1.0
CG C:GLU101 3.4 60.0 1.0
CE1 C:HIS33 3.4 66.7 1.0
OE1 C:GLU101 3.9 67.3 1.0
CG C:GLU81 4.2 57.2 1.0
ND1 C:HIS88 4.3 69.1 1.0
CG C:HIS88 4.3 66.9 1.0
ND1 C:HIS90 4.3 52.2 1.0
CG C:HIS90 4.5 51.6 1.0
CG C:HIS33 4.5 65.6 1.0
ND1 C:HIS33 4.5 67.7 1.0
NE2 C:HIS71 4.7 64.5 1.0
CB C:GLU101 4.8 57.5 1.0
CB C:GLU81 4.9 56.5 1.0

Manganese binding site 3 out of 4 in 4rb3

Go back to Manganese Binding Sites List in 4rb3
Manganese binding site 3 out of 4 in the Crystal Structure of Magnetospirillum Gryphiswaldense Msr-1 Fur-MN2+- FEOAB1 Operator


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Magnetospirillum Gryphiswaldense Msr-1 Fur-MN2+- FEOAB1 Operator within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn201

b:54.2
occ:1.00
OD1 D:ASP89 2.0 54.6 1.0
OE1 D:GLU108 2.0 54.4 1.0
NE2 D:HIS87 2.1 54.5 1.0
O D:HOH304 2.1 48.2 1.0
NE2 D:HIS125 2.2 54.0 1.0
OD2 D:ASP89 2.4 56.1 1.0
CG D:ASP89 2.5 57.8 1.0
CE1 D:HIS87 2.9 53.5 1.0
CE1 D:HIS125 3.1 53.1 1.0
CD D:GLU108 3.1 61.4 1.0
CD2 D:HIS87 3.2 55.6 1.0
CD2 D:HIS125 3.3 53.7 1.0
OE2 D:GLU108 3.6 68.7 1.0
CB D:ASP89 4.0 56.6 1.0
ND1 D:HIS87 4.1 53.1 1.0
CG D:HIS87 4.3 54.4 1.0
ND1 D:HIS125 4.3 56.5 1.0
O D:HOH306 4.3 58.9 1.0
CG D:GLU108 4.3 60.1 1.0
CG D:HIS125 4.4 56.9 1.0
NE2 D:GLN111 4.5 54.3 1.0
N D:ASP89 4.6 55.6 1.0
OE1 D:GLN111 4.7 54.7 1.0
CA D:ASP89 4.8 56.8 1.0
C D:HIS88 4.8 53.1 1.0
CB D:LEU127 5.0 54.1 1.0
O D:HIS88 5.0 53.0 1.0

Manganese binding site 4 out of 4 in 4rb3

Go back to Manganese Binding Sites List in 4rb3
Manganese binding site 4 out of 4 in the Crystal Structure of Magnetospirillum Gryphiswaldense Msr-1 Fur-MN2+- FEOAB1 Operator


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Magnetospirillum Gryphiswaldense Msr-1 Fur-MN2+- FEOAB1 Operator within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn202

b:62.2
occ:1.00
NE2 D:HIS88 2.1 47.4 1.0
NE2 D:HIS33 2.3 65.3 1.0
NE2 D:HIS90 2.3 57.0 1.0
OE1 D:GLU81 2.4 64.0 1.0
OE2 D:GLU101 2.6 75.8 1.0
OE2 D:GLU81 2.6 60.6 1.0
CD D:GLU81 2.8 63.0 1.0
CE1 D:HIS33 2.9 68.5 1.0
CE1 D:HIS88 2.9 48.5 1.0
CE1 D:HIS90 3.2 57.0 1.0
CD2 D:HIS90 3.2 56.2 1.0
CD2 D:HIS88 3.3 49.6 1.0
CD D:GLU101 3.3 72.9 1.0
CG D:GLU101 3.5 67.4 1.0
CD2 D:HIS33 3.5 69.2 1.0
ND1 D:HIS88 4.1 49.1 1.0
ND1 D:HIS33 4.2 68.5 1.0
CG D:HIS88 4.3 50.5 1.0
CG D:GLU81 4.3 61.9 1.0
ND1 D:HIS90 4.3 56.0 1.0
OE1 D:GLU101 4.4 73.6 1.0
CG D:HIS90 4.4 55.6 1.0
CG D:HIS33 4.5 67.6 1.0
NE2 D:HIS71 4.5 61.7 1.0
CB D:GLU101 4.7 64.6 1.0
CB D:GLU81 4.9 61.7 1.0

Reference:

Z.Deng, Q.Wang, Z.Liu, M.Zhang, A.C.Machado, T.P.Chiu, C.Feng, Q.Zhang, L.Yu, L.Qi, J.Zheng, X.Wang, X.Huo, X.Qi, X.Li, W.Wu, R.Rohs, Y.Li, Z.Chen. Mechanistic Insights Into Metal Ion Activation and Operator Recognition By the Ferric Uptake Regulator. Nat Commun V. 6 7642.
ISSN: ESSN 2041-1723
PubMed: 26134419
DOI: 10.1038/NCOMMS8642
Page generated: Tue Dec 15 04:28:47 2020

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