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Manganese in PDB 1bcf: The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site

Protein crystallography data

The structure of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site, PDB code: 1bcf was solved by F.Frolow, A.J.Kalb(Gilboa), J.Yariv, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.90
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 211.100, 211.100, 145.200, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / n/a

Other elements in 1bcf:

The structure of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site also contains other interesting chemical elements:

Iron (Fe) 6 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Manganese atom in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site (pdb code 1bcf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 24 binding sites of Manganese where determined in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site, PDB code: 1bcf:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 24 in 1bcf

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Manganese binding site 1 out of 24 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn600

b:11.7
occ:1.00
 ND1 A:HIS130 1.9 7.3 1.0
OE2 A:GLU94 2.0 12.0 1.0
OE1 A:GLU127 2.0 4.2 1.0
OE2 A:GLU51 2.1 12.3 1.0
CE1 A:HIS130 2.6 8.5 1.0
CD A:GLU94 2.7 10.3 1.0
OE1 A:GLU94 2.8 14.8 1.0
CD A:GLU51 3.1 9.0 1.0
CG A:HIS130 3.1 9.5 1.0
CD A:GLU127 3.2 5.1 1.0
OE1 A:GLU51 3.3 9.8 1.0
CB A:HIS130 3.7 6.9 1.0
OE2 A:GLU127 3.7 5.6 1.0
NE2 A:HIS130 3.9 8.2 1.0
CD2 A:HIS130 4.1 9.1 1.0
MN A:MN601 4.1 2.9 1.0
CG A:GLU94 4.2 8.1 1.0
CA A:GLU127 4.2 3.6 1.0
OH A:TYR25 4.3 16.4 1.0
CE2 A:TYR25 4.3 13.8 1.0
CG A:GLU127 4.4 2.0 1.0
CG A:GLU51 4.4 8.1 1.0
CB A:GLU127 4.5 2.5 1.0
O A:GLU127 4.8 2.8 1.0
CZ A:TYR25 4.8 15.0 1.0

Manganese binding site 2 out of 24 in 1bcf

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Manganese binding site 2 out of 24 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:2.9
occ:1.00
 ND1 A:HIS54 1.8 2.6 1.0
OE2 A:GLU127 2.0 5.6 1.0
OE1 A:GLU51 2.0 9.8 1.0
OE2 A:GLU18 2.1 10.3 1.0
OE1 A:GLU18 2.6 12.4 1.0
CD A:GLU18 2.7 8.5 1.0
CE1 A:HIS54 2.7 2.0 1.0
CG A:HIS54 2.9 3.6 1.0
CD A:GLU127 3.1 5.1 1.0
CD A:GLU51 3.3 9.0 1.0
CB A:HIS54 3.3 2.0 1.0
OE1 A:GLU127 3.4 4.2 1.0
OE2 A:GLU51 3.8 12.3 1.0
NE2 A:HIS54 3.9 2.0 1.0
CD2 A:HIS54 3.9 2.0 1.0
CA A:GLU51 4.0 6.0 1.0
MN A:MN600 4.1 11.7 1.0
CG A:GLU18 4.2 5.9 1.0
CG2 A:ILE123 4.4 2.0 1.0
CG A:GLU127 4.4 2.0 1.0
CG A:GLU51 4.4 8.1 1.0
CB A:GLU51 4.5 6.2 1.0
O A:GLU51 4.7 5.6 1.0
CE1 A:HIS130 4.8 8.5 1.0
N A:GLU51 4.8 4.4 1.0
CA A:HIS54 4.8 2.0 1.0
C A:GLU51 4.9 5.0 1.0

Manganese binding site 3 out of 24 in 1bcf

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Manganese binding site 3 out of 24 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn600

b:12.6
occ:1.00
 ND1 B:HIS130 1.8 6.9 1.0
OE2 B:GLU94 2.0 12.4 1.0
OE1 B:GLU127 2.0 6.6 1.0
OE2 B:GLU51 2.1 11.0 1.0
CE1 B:HIS130 2.6 9.3 1.0
CD B:GLU94 2.7 12.2 1.0
OE1 B:GLU94 2.7 15.8 1.0
CG B:HIS130 3.1 9.3 1.0
CD B:GLU51 3.1 8.3 1.0
CD B:GLU127 3.2 4.5 1.0
OE1 B:GLU51 3.4 9.7 1.0
CB B:HIS130 3.6 6.5 1.0
OE2 B:GLU127 3.8 4.9 1.0
NE2 B:HIS130 3.9 10.4 1.0
CD2 B:HIS130 4.1 10.7 1.0
MN B:MN601 4.1 8.1 1.0
CG B:GLU94 4.2 9.2 1.0
CA B:GLU127 4.2 2.7 1.0
OH B:TYR25 4.3 15.3 1.0
CE2 B:TYR25 4.4 13.6 1.0
CG B:GLU127 4.4 2.0 1.0
CB B:GLU127 4.4 3.2 1.0
CG B:GLU51 4.5 6.6 1.0
O B:GLU127 4.8 3.1 1.0
CZ B:TYR25 4.8 14.9 1.0
C B:GLU127 5.0 3.1 1.0
N B:GLU127 5.0 4.3 1.0

Manganese binding site 4 out of 24 in 1bcf

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Manganese binding site 4 out of 24 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn601

b:8.1
occ:1.00
 ND1 B:HIS54 1.8 2.6 1.0
OE1 B:GLU51 2.0 9.7 1.0
OE2 B:GLU127 2.0 4.9 1.0
OE2 B:GLU18 2.2 9.2 1.0
OE1 B:GLU18 2.6 11.3 1.0
CD B:GLU18 2.7 8.6 1.0
CE1 B:HIS54 2.7 2.0 1.0
CG B:HIS54 2.9 3.8 1.0
CD B:GLU127 3.1 4.5 1.0
CD B:GLU51 3.2 8.3 1.0
CB B:HIS54 3.4 2.0 1.0
OE1 B:GLU127 3.4 6.6 1.0
OE2 B:GLU51 3.8 11.0 1.0
NE2 B:HIS54 3.9 2.0 1.0
CD2 B:HIS54 3.9 2.0 1.0
CA B:GLU51 4.0 3.5 1.0
MN B:MN600 4.1 12.6 1.0
CG B:GLU18 4.2 7.4 1.0
CG2 B:ILE123 4.4 2.0 1.0
CG B:GLU127 4.4 2.0 1.0
CG B:GLU51 4.4 6.6 1.0
CB B:GLU51 4.5 3.7 1.0
CE1 B:HIS130 4.7 9.3 1.0
O B:GLU51 4.8 5.2 1.0
N B:GLU51 4.8 3.9 1.0
CA B:HIS54 4.9 2.0 1.0
C B:GLU51 4.9 4.8 1.0

Manganese binding site 5 out of 24 in 1bcf

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Manganese binding site 5 out of 24 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn600

b:11.7
occ:1.00
 ND1 C:HIS130 1.9 7.3 1.0
OE2 C:GLU94 2.0 12.0 1.0
OE1 C:GLU127 2.0 4.2 1.0
OE2 C:GLU51 2.1 12.3 1.0
CE1 C:HIS130 2.6 8.5 1.0
CD C:GLU94 2.7 10.3 1.0
OE1 C:GLU94 2.8 14.8 1.0
CD C:GLU51 3.1 9.0 1.0
CG C:HIS130 3.1 9.5 1.0
CD C:GLU127 3.2 5.1 1.0
OE1 C:GLU51 3.3 9.8 1.0
CB C:HIS130 3.7 6.9 1.0
OE2 C:GLU127 3.7 5.6 1.0
NE2 C:HIS130 3.9 8.2 1.0
CD2 C:HIS130 4.1 9.1 1.0
MN C:MN601 4.1 2.9 1.0
CG C:GLU94 4.2 8.1 1.0
CA C:GLU127 4.2 3.6 1.0
OH C:TYR25 4.3 16.4 1.0
CE2 C:TYR25 4.3 13.8 1.0
CG C:GLU127 4.4 2.0 1.0
CG C:GLU51 4.4 8.1 1.0
CB C:GLU127 4.5 2.5 1.0
O C:GLU127 4.8 2.8 1.0
CZ C:TYR25 4.8 15.0 1.0

Manganese binding site 6 out of 24 in 1bcf

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Manganese binding site 6 out of 24 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn601

b:2.9
occ:1.00
 ND1 C:HIS54 1.8 2.6 1.0
OE2 C:GLU127 2.0 5.6 1.0
OE1 C:GLU51 2.0 9.8 1.0
OE2 C:GLU18 2.1 10.3 1.0
OE1 C:GLU18 2.6 12.4 1.0
CD C:GLU18 2.7 8.5 1.0
CE1 C:HIS54 2.7 2.0 1.0
CG C:HIS54 2.9 3.6 1.0
CD C:GLU127 3.1 5.1 1.0
CD C:GLU51 3.3 9.0 1.0
CB C:HIS54 3.3 2.0 1.0
OE1 C:GLU127 3.4 4.2 1.0
OE2 C:GLU51 3.8 12.3 1.0
NE2 C:HIS54 3.9 2.0 1.0
CD2 C:HIS54 3.9 2.0 1.0
CA C:GLU51 4.0 6.0 1.0
MN C:MN600 4.1 11.7 1.0
CG C:GLU18 4.2 5.9 1.0
CG2 C:ILE123 4.4 2.0 1.0
CG C:GLU127 4.4 2.0 1.0
CG C:GLU51 4.4 8.1 1.0
CB C:GLU51 4.5 6.2 1.0
O C:GLU51 4.7 5.6 1.0
CE1 C:HIS130 4.8 8.5 1.0
N C:GLU51 4.8 4.4 1.0
CA C:HIS54 4.8 2.0 1.0
C C:GLU51 4.9 5.0 1.0

Manganese binding site 7 out of 24 in 1bcf

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Manganese binding site 7 out of 24 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn600

b:12.6
occ:1.00
 ND1 D:HIS130 1.8 6.9 1.0
OE2 D:GLU94 2.0 12.4 1.0
OE1 D:GLU127 2.0 6.6 1.0
OE2 D:GLU51 2.1 11.0 1.0
CE1 D:HIS130 2.6 9.3 1.0
CD D:GLU94 2.7 12.2 1.0
OE1 D:GLU94 2.7 15.8 1.0
CG D:HIS130 3.1 9.3 1.0
CD D:GLU51 3.1 8.3 1.0
CD D:GLU127 3.2 4.5 1.0
OE1 D:GLU51 3.4 9.7 1.0
CB D:HIS130 3.6 6.5 1.0
OE2 D:GLU127 3.8 4.9 1.0
NE2 D:HIS130 3.9 10.4 1.0
CD2 D:HIS130 4.1 10.7 1.0
MN D:MN601 4.1 8.1 1.0
CG D:GLU94 4.1 9.2 1.0
CA D:GLU127 4.2 2.7 1.0
OH D:TYR25 4.3 15.3 1.0
CE2 D:TYR25 4.4 13.6 1.0
CG D:GLU127 4.4 2.0 1.0
CB D:GLU127 4.4 3.2 1.0
CG D:GLU51 4.5 6.6 1.0
O D:GLU127 4.8 3.1 1.0
CZ D:TYR25 4.8 14.9 1.0
C D:GLU127 5.0 3.1 1.0
N D:GLU127 5.0 4.3 1.0

Manganese binding site 8 out of 24 in 1bcf

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Manganese binding site 8 out of 24 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn601

b:8.1
occ:1.00
 ND1 D:HIS54 1.8 2.6 1.0
OE1 D:GLU51 2.0 9.7 1.0
OE2 D:GLU127 2.0 4.9 1.0
OE2 D:GLU18 2.2 9.2 1.0
OE1 D:GLU18 2.6 11.3 1.0
CD D:GLU18 2.7 8.6 1.0
CE1 D:HIS54 2.7 2.0 1.0
CG D:HIS54 2.9 3.8 1.0
CD D:GLU127 3.1 4.5 1.0
CD D:GLU51 3.2 8.3 1.0
CB D:HIS54 3.4 2.0 1.0
OE1 D:GLU127 3.4 6.6 1.0
OE2 D:GLU51 3.8 11.0 1.0
NE2 D:HIS54 3.9 2.0 1.0
CD2 D:HIS54 3.9 2.0 1.0
CA D:GLU51 4.0 3.5 1.0
MN D:MN600 4.1 12.6 1.0
CG D:GLU18 4.2 7.4 1.0
CG2 D:ILE123 4.4 2.0 1.0
CG D:GLU127 4.4 2.0 1.0
CG D:GLU51 4.4 6.6 1.0
CB D:GLU51 4.5 3.7 1.0
CE1 D:HIS130 4.7 9.3 1.0
O D:GLU51 4.8 5.2 1.0
N D:GLU51 4.8 3.9 1.0
CA D:HIS54 4.9 2.0 1.0
C D:GLU51 4.9 4.8 1.0

Manganese binding site 9 out of 24 in 1bcf

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Manganese binding site 9 out of 24 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn600

b:11.7
occ:1.00
 ND1 E:HIS130 1.9 7.3 1.0
OE2 E:GLU94 2.0 12.0 1.0
OE1 E:GLU127 2.0 4.2 1.0
OE2 E:GLU51 2.1 12.3 1.0
CE1 E:HIS130 2.6 8.5 1.0
CD E:GLU94 2.7 10.3 1.0
OE1 E:GLU94 2.8 14.8 1.0
CD E:GLU51 3.1 9.0 1.0
CG E:HIS130 3.1 9.5 1.0
CD E:GLU127 3.2 5.1 1.0
OE1 E:GLU51 3.3 9.8 1.0
CB E:HIS130 3.7 6.9 1.0
OE2 E:GLU127 3.7 5.6 1.0
NE2 E:HIS130 3.9 8.2 1.0
CD2 E:HIS130 4.1 9.1 1.0
MN E:MN601 4.1 2.9 1.0
CG E:GLU94 4.2 8.1 1.0
CA E:GLU127 4.2 3.6 1.0
OH E:TYR25 4.3 16.4 1.0
CE2 E:TYR25 4.3 13.8 1.0
CG E:GLU127 4.4 2.0 1.0
CG E:GLU51 4.4 8.1 1.0
CB E:GLU127 4.5 2.5 1.0
O E:GLU127 4.8 2.8 1.0
CZ E:TYR25 4.8 15.0 1.0

Manganese binding site 10 out of 24 in 1bcf

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Manganese binding site 10 out of 24 in the The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of The Structure of A Unique, Two-Fold Symmetric, Haem-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn601

b:2.9
occ:1.00
 ND1 E:HIS54 1.8 2.6 1.0
OE2 E:GLU127 2.0 5.6 1.0
OE1 E:GLU51 2.0 9.8 1.0
OE2 E:GLU18 2.1 10.3 1.0
OE1 E:GLU18 2.6 12.4 1.0
CD E:GLU18 2.7 8.5 1.0
CE1 E:HIS54 2.7 2.0 1.0
CG E:HIS54 2.9 3.6 1.0
CD E:GLU127 3.1 5.1 1.0
CD E:GLU51 3.3 9.0 1.0
CB E:HIS54 3.3 2.0 1.0
OE1 E:GLU127 3.4 4.2 1.0
OE2 E:GLU51 3.8 12.3 1.0
NE2 E:HIS54 3.9 2.0 1.0
CD2 E:HIS54 3.9 2.0 1.0
CA E:GLU51 4.0 6.0 1.0
MN E:MN600 4.1 11.7 1.0
CG E:GLU18 4.2 5.9 1.0
CG2 E:ILE123 4.4 2.0 1.0
CG E:GLU127 4.4 2.0 1.0
CG E:GLU51 4.4 8.1 1.0
CB E:GLU51 4.5 6.2 1.0
O E:GLU51 4.7 5.6 1.0
CE1 E:HIS130 4.8 8.5 1.0
N E:GLU51 4.8 4.4 1.0
CA E:HIS54 4.8 2.0 1.0
C E:GLU51 4.9 5.0 1.0
O E:ASP50 5.0 4.4 1.0

Reference:

F.Frolow, A.J.Kalb, J.Yariv. Structure of A Unique Twofold Symmetric Haem-Binding Site. Nat.Struct.Biol. V. 1 453 1994.
ISSN: ISSN 1072-8368
PubMed: 7664064
DOI: 10.1038/NSB0794-453
Page generated: Sat Oct 5 09:46:57 2024

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