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Manganese in PDB 1jm0: Crystal Structure of Four-Helix Bundle Model

Protein crystallography data

The structure of Crystal Structure of Four-Helix Bundle Model, PDB code: 1jm0 was solved by L.Di Costanzo, S.Geremia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.10 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.380, 80.120, 99.930, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.8

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Four-Helix Bundle Model (pdb code 1jm0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Crystal Structure of Four-Helix Bundle Model, PDB code: 1jm0:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 1jm0

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Manganese binding site 1 out of 12 in the Crystal Structure of Four-Helix Bundle Model


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Four-Helix Bundle Model within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:16.0
occ:1.00
 OE1 A:GLU36 2.0 15.8 1.0
OE2 B:GLU36 2.1 19.1 1.0
OE2 A:GLU10 2.3 16.3 1.0
OE1 A:GLU10 2.3 18.4 1.0
ND1 A:HIS39 2.3 17.1 1.0
O B:DMS301 2.4 23.5 0.5
O B:DMS301 2.4 18.9 0.5
CD A:GLU10 2.6 17.4 1.0
CD B:GLU36 3.0 18.0 1.0
CD A:GLU36 3.0 11.4 1.0
OE1 B:GLU36 3.1 20.6 1.0
CE1 A:HIS39 3.1 18.0 1.0
S B:DMS301 3.4 25.0 0.5
CG A:HIS39 3.4 15.1 1.0
S B:DMS301 3.5 19.8 0.5
MN B:MN402 3.7 16.2 1.0
OE2 A:GLU36 3.7 16.9 1.0
C1 B:DMS301 3.8 23.2 0.5
CB A:HIS39 3.8 13.9 1.0
C2 B:DMS301 3.9 18.7 0.5
CG A:GLU10 4.2 16.4 1.0
CA A:GLU36 4.2 14.8 1.0
CG A:GLU36 4.2 12.5 1.0
CB A:GLU36 4.3 13.6 1.0
NE2 A:HIS39 4.3 15.1 1.0
CG B:GLU36 4.4 17.7 1.0
CD2 A:HIS39 4.5 14.2 1.0
CG2 B:ILE32 4.5 14.8 1.0
OH B:TYR17 4.6 20.4 1.0
CE1 B:HIS39 4.7 15.0 1.0
CE1 B:TYR17 4.8 22.0 1.0
ND1 B:HIS39 4.8 16.0 1.0
C2 B:DMS301 4.9 24.3 0.5
N A:GLU36 4.9 16.9 1.0
C1 B:DMS301 5.0 20.2 0.5

Manganese binding site 2 out of 12 in 1jm0

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Manganese binding site 2 out of 12 in the Crystal Structure of Four-Helix Bundle Model


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 Four-Helix Bundle Model within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:16.2
occ:1.00
 OE1 B:GLU36 2.0 20.6 1.0
OE2 A:GLU36 2.1 16.9 1.0
OE2 B:GLU10 2.1 15.3 1.0
ND1 B:HIS39 2.2 16.0 1.0
OE1 B:GLU10 2.3 18.6 1.0
O B:DMS301 2.4 23.5 0.5
O B:DMS301 2.4 18.9 0.5
CD B:GLU10 2.6 16.1 1.0
CD A:GLU36 2.9 11.4 1.0
CE1 B:HIS39 3.1 15.0 1.0
CD B:GLU36 3.1 18.0 1.0
OE1 A:GLU36 3.1 15.8 1.0
CG B:HIS39 3.3 16.3 1.0
S B:DMS301 3.4 19.8 0.5
S B:DMS301 3.5 25.0 0.5
MN A:MN401 3.7 16.0 1.0
OE2 B:GLU36 3.7 19.1 1.0
CB B:HIS39 3.7 16.9 1.0
C2 B:DMS301 3.8 24.3 0.5
C1 B:DMS301 3.8 20.2 0.5
CG B:GLU10 4.1 21.6 1.0
NE2 B:HIS39 4.3 16.4 1.0
CG A:GLU36 4.3 12.5 1.0
CG B:GLU36 4.3 17.7 1.0
CG2 A:ILE32 4.4 15.2 1.0
CA B:GLU36 4.4 17.3 1.0
CD2 B:HIS39 4.4 15.4 1.0
CB B:GLU36 4.6 17.8 1.0
OH A:TYR17 4.6 21.4 1.0
CE1 A:TYR17 4.7 16.0 1.0
C1 B:DMS301 4.9 23.2 0.5
C2 B:DMS301 5.0 18.7 0.5
CB B:GLU10 5.0 20.4 1.0

Manganese binding site 3 out of 12 in 1jm0

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Manganese binding site 3 out of 12 in the Crystal Structure of Four-Helix Bundle Model


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 Four-Helix Bundle Model within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:38.6
occ:1.00
 O B:HOH506 2.0 39.2 1.0
O B:HOH507 2.1 38.8 1.0
OE1 B:GLU19 2.1 29.6 1.0
O B:HOH505 2.1 37.7 1.0
OE1 B:GLN16 2.2 28.4 1.0
CD B:GLU19 3.1 27.8 1.0
CD B:GLN16 3.2 26.1 1.0
NE2 B:GLN16 3.5 29.0 1.0
OE2 B:GLU19 3.5 31.7 1.0
O B:HOH521 4.2 56.7 1.0
O A:HOH433 4.3 38.3 1.0
O B:HOH511 4.4 36.6 1.0
CG B:GLU19 4.4 30.9 1.0
CG B:GLN16 4.6 23.5 1.0
CB B:GLU19 4.6 29.5 1.0
O B:HOH532 4.9 46.9 1.0
CB B:GLN16 4.9 24.4 1.0
CA B:GLN16 5.0 22.6 1.0

Manganese binding site 4 out of 12 in 1jm0

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Manganese binding site 4 out of 12 in the Crystal Structure of Four-Helix Bundle Model


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 Four-Helix Bundle Model within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn403

b:16.9
occ:1.00
 OE2 D:GLU36 2.0 20.9 1.0
OE1 C:GLU36 2.1 17.1 1.0
ND1 C:HIS39 2.2 14.1 1.0
OE2 C:GLU10 2.2 15.4 1.0
OE1 C:GLU10 2.4 15.4 1.0
O C:DMS302 2.4 21.5 1.0
CD C:GLU10 2.6 14.5 1.0
CD D:GLU36 3.0 17.9 1.0
CE1 C:HIS39 3.0 19.4 1.0
CD C:GLU36 3.1 17.8 1.0
OE1 D:GLU36 3.2 21.1 1.0
CG C:HIS39 3.3 17.3 1.0
S C:DMS302 3.4 26.7 1.0
MN D:MN404 3.6 17.4 1.0
OE2 C:GLU36 3.7 20.3 1.0
CB C:HIS39 3.8 15.2 1.0
C1 C:DMS302 3.9 23.3 1.0
CG C:GLU10 4.1 17.4 1.0
CA C:GLU36 4.1 18.3 1.0
NE2 C:HIS39 4.2 13.9 1.0
CG C:GLU36 4.3 18.6 1.0
CB C:GLU36 4.3 16.6 1.0
CD2 C:HIS39 4.4 15.5 1.0
CG D:GLU36 4.4 17.4 1.0
OH D:TYR17 4.6 16.9 1.0
CG2 D:ILE32 4.7 16.2 1.0
CE1 D:HIS39 4.7 17.4 1.0
CE1 D:TYR17 4.7 17.8 1.0
ND1 D:HIS39 4.8 13.3 1.0
C2 C:DMS302 4.9 25.2 1.0
N C:GLU36 4.9 16.9 1.0
CB C:GLU10 5.0 16.9 1.0

Manganese binding site 5 out of 12 in 1jm0

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Manganese binding site 5 out of 12 in the Crystal Structure of Four-Helix Bundle Model


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Four-Helix Bundle Model within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:32.1
occ:0.50
 MN C:MN505 0.0 32.1 0.5
OE1 C:GLN16 2.1 43.9 1.0
O C:HOH507 2.1 42.8 1.0
O C:HOH508 2.3 41.5 1.0
OE1 C:GLU19 2.8 51.2 1.0
CD C:GLN16 3.1 40.0 1.0
NE2 C:GLN16 3.4 42.4 1.0
MN C:MN505 3.6 46.9 0.5
CD C:GLU19 4.0 47.8 1.0
O C:HOH512 4.1 27.2 1.0
O D:HOH511 4.3 29.4 1.0
CG C:GLN16 4.5 33.5 1.0
OE2 C:GLU19 4.5 49.0 1.0
O C:HOH524 4.9 54.3 1.0
CB C:GLN16 4.9 26.7 1.0

Manganese binding site 6 out of 12 in 1jm0

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Manganese binding site 6 out of 12 in the Crystal Structure of Four-Helix Bundle Model


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Four-Helix Bundle Model within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:46.9
occ:0.50
 MN C:MN505 0.0 46.9 0.5
OE1 C:GLU19 2.3 51.2 1.0
CD C:GLU19 3.0 47.8 1.0
O C:HOH507 3.2 42.8 1.0
OE2 C:GLU19 3.4 49.0 1.0
MN C:MN505 3.6 32.1 0.5
CG C:GLU19 4.0 40.9 1.0
CB C:GLU19 4.7 34.2 1.0

Manganese binding site 7 out of 12 in 1jm0

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Manganese binding site 7 out of 12 in the Crystal Structure of Four-Helix Bundle Model


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Four-Helix Bundle Model within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn404

b:17.4
occ:1.00
 OE2 C:GLU36 2.1 20.3 1.0
OE1 D:GLU36 2.1 21.1 1.0
ND1 D:HIS39 2.2 13.3 1.0
OE1 D:GLU10 2.3 19.9 1.0
OE2 D:GLU10 2.3 15.0 1.0
O C:DMS302 2.3 21.5 1.0
CD D:GLU10 2.6 15.0 1.0
CD C:GLU36 2.9 17.8 1.0
OE1 C:GLU36 2.9 17.1 1.0
CE1 D:HIS39 3.1 17.4 1.0
CD D:GLU36 3.2 17.9 1.0
CG D:HIS39 3.3 15.0 1.0
S C:DMS302 3.5 26.7 1.0
MN C:MN403 3.6 16.9 1.0
OE2 D:GLU36 3.7 20.9 1.0
C2 C:DMS302 3.7 25.2 1.0
CB D:HIS39 3.8 17.9 1.0
CG D:GLU10 4.1 19.6 1.0
NE2 D:HIS39 4.3 14.9 1.0
O D:HOH513 4.3 27.3 1.0
CG C:GLU36 4.3 18.6 1.0
CD2 D:HIS39 4.4 17.9 1.0
CG2 C:ILE32 4.5 19.0 1.0
CG D:GLU36 4.5 17.4 1.0
CA D:GLU36 4.5 16.2 1.0
CB D:GLU36 4.7 16.7 1.0
OH C:TYR17 4.7 18.2 1.0
CE1 C:HIS39 4.9 19.4 1.0
CE1 C:TYR17 4.9 15.0 1.0
CB D:GLU10 4.9 20.0 1.0
C1 C:DMS302 4.9 23.3 1.0
ND1 C:HIS39 4.9 14.1 1.0

Manganese binding site 8 out of 12 in 1jm0

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Manganese binding site 8 out of 12 in the Crystal Structure of Four-Helix Bundle Model


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Four-Helix Bundle Model within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:23.5
occ:1.00
 OE1 D:GLU19 2.0 28.5 1.0
O C:HOH506 2.0 27.4 1.0
O D:HOH505 2.1 28.6 1.0
OE1 F:GLU34 2.1 23.3 1.0
OE1 D:GLN16 2.1 22.7 1.0
O F:HOH407 2.1 24.5 1.0
CD D:GLU19 3.0 26.4 1.0
CD F:GLU34 3.0 27.8 1.0
CD D:GLN16 3.1 21.0 1.0
OE2 F:GLU34 3.2 29.2 1.0
OE2 D:GLU19 3.3 27.1 1.0
NE2 D:GLN16 3.5 23.7 1.0
O F:HOH409 4.0 26.2 1.0
O D:HOH516 4.0 32.7 1.0
O C:HOH543 4.1 33.2 1.0
O D:HOH558 4.2 32.1 1.0
CG D:GLU19 4.3 24.1 1.0
OE1 C:GLU5 4.3 45.2 1.0
CG F:GLU34 4.4 20.4 1.0
O F:HOH437 4.4 35.1 1.0
CG D:GLN16 4.5 17.7 1.0
O C:HOH526 4.5 44.7 1.0
CB D:GLU19 4.9 23.2 1.0
CB D:GLN16 4.9 21.0 1.0

Manganese binding site 9 out of 12 in 1jm0

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Manganese binding site 9 out of 12 in the Crystal Structure of Four-Helix Bundle Model


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Four-Helix Bundle Model within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn504

b:49.0
occ:1.00
 O D:HOH506 2.0 45.5 1.0
O D:HOH508 2.0 48.2 1.0
O D:HOH507 2.0 49.8 1.0
OE1 D:GLU37 2.1 37.5 1.0
OE1 D:GLU34 2.2 37.1 1.0
CD D:GLU34 3.0 33.8 1.0
OE2 D:GLU34 3.0 38.1 1.0
CD D:GLU37 3.2 34.2 1.0
OE2 D:GLU37 3.7 33.1 1.0
O D:HOH522 4.0 25.3 1.0
CG D:GLU34 4.4 23.2 1.0
CG D:GLU37 4.5 25.4 1.0
CB D:GLU37 4.7 18.1 1.0
CA D:GLU34 4.9 16.9 1.0
CB D:GLU34 5.0 19.5 1.0

Manganese binding site 10 out of 12 in 1jm0

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Manganese binding site 10 out of 12 in the Crystal Structure of Four-Helix Bundle Model


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Four-Helix Bundle Model within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn405

b:15.9
occ:1.00
 OE2 F:GLU36 2.1 16.2 1.0
OE1 E:GLU36 2.1 20.3 1.0
OE1 E:GLU10 2.2 15.2 1.0
ND1 E:HIS39 2.2 15.2 1.0
OE2 E:GLU10 2.3 17.6 1.0
O F:DMS303 2.5 22.9 1.0
CD E:GLU10 2.6 19.1 1.0
CD F:GLU36 2.9 11.0 1.0
C1 F:DMS303 3.1 17.8 1.0
CE1 E:HIS39 3.1 15.0 1.0
CD E:GLU36 3.2 14.2 1.0
OE1 F:GLU36 3.2 16.0 1.0
CG E:HIS39 3.3 14.3 1.0
S F:DMS303 3.4 29.0 1.0
CB E:HIS39 3.7 14.3 1.0
OE2 E:GLU36 3.7 15.9 1.0
MN F:MN406 3.9 15.4 1.0
CG E:GLU10 4.1 16.2 1.0
CG2 F:ILE32 4.2 16.6 1.0
CG F:GLU36 4.3 9.7 1.0
NE2 E:HIS39 4.3 15.1 1.0
CA E:GLU36 4.3 13.8 1.0
CG E:GLU36 4.3 12.6 1.0
CD2 E:HIS39 4.4 14.2 1.0
CB E:GLU36 4.5 14.0 1.0
OH F:TYR17 4.8 15.7 1.0
CB E:GLU10 4.9 16.5 1.0
N E:GLU36 5.0 14.1 1.0
C2 F:DMS303 5.0 22.2 1.0

Reference:

L.Di Costanzo, H.Wade, S.Geremia, L.Randaccio, V.Pavone, W.F.Degrado, A.Lombardi. Toward the De Novo Design of A Catalytically Active Helix Bundle: A Substrate-Accessible Carboxylate-Bridged Dinuclear Metal Center. J.Am.Chem.Soc. V. 123 12749 2001.
ISSN: ISSN 0002-7863
PubMed: 11749531
DOI: 10.1021/JA010506X
Page generated: Sat Oct 5 11:11:42 2024

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