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Cobalt in PDB 2dfi: Crystal Structure of Pf-Map(1-292)-C

Enzymatic activity of Crystal Structure of Pf-Map(1-292)-C

All present enzymatic activity of Crystal Structure of Pf-Map(1-292)-C:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Pf-Map(1-292)-C, PDB code: 2dfi was solved by Y.Katagiri, K.Takano, H.Chon, H.Matsumura, Y.Koga, S.Kanaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.19 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.650, 81.071, 51.350, 90.00, 105.62, 90.00
R / Rfree (%) 20.3 / 25.2

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Pf-Map(1-292)-C (pdb code 2dfi). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Crystal Structure of Pf-Map(1-292)-C, PDB code: 2dfi:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in 2dfi

Go back to Cobalt Binding Sites List in 2dfi
Cobalt binding site 1 out of 6 in the Crystal Structure of Pf-Map(1-292)-C


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Pf-Map(1-292)-C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co504

b:18.1
occ:1.00
 OD2 A:ASP82 2.1 17.7 1.0
OE1 A:GLU280 2.2 15.1 1.0
OD1 A:ASP93 2.2 17.5 1.0
OD1 A:ASP82 2.3 14.9 1.0
CG A:ASP82 2.5 16.5 1.0
CG A:ASP93 2.9 12.6 1.0
OD2 A:ASP93 2.9 14.1 1.0
CD A:GLU280 3.0 9.5 1.0
CO A:CO505 3.0 17.0 1.0
OE2 A:GLU280 3.1 11.9 1.0
OE1 A:GLU187 3.8 25.4 1.0
CB A:ASP82 4.0 16.5 1.0
CZ A:PHE50 4.1 18.1 1.0
O A:THR94 4.1 14.7 1.0
CD A:GLU187 4.2 21.1 1.0
CB A:ASP93 4.3 16.4 1.0
CG A:GLU280 4.4 13.8 1.0
NE2 A:GLN278 4.4 14.0 1.0
OE2 A:GLU187 4.5 19.7 1.0
N A:THR94 4.5 15.0 1.0
C A:THR94 4.6 15.9 1.0
CE1 A:PHE50 4.6 18.9 1.0
CB A:ALA95 4.6 16.6 1.0
C A:ASP93 4.6 16.3 1.0
CA A:ASP82 4.8 17.9 1.0
CA A:ASP93 4.8 17.3 1.0
CA A:THR94 4.9 17.4 1.0
CB A:GLU280 4.9 12.4 1.0
CE2 A:PHE50 5.0 17.6 1.0

Cobalt binding site 2 out of 6 in 2dfi

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Cobalt binding site 2 out of 6 in the Crystal Structure of Pf-Map(1-292)-C


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Pf-Map(1-292)-C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co505

b:17.0
occ:1.00
 OE2 A:GLU280 2.1 11.9 1.0
OD2 A:ASP93 2.2 14.1 1.0
NE2 A:HIS153 2.3 16.0 1.0
OE2 A:GLU187 2.4 19.7 1.0
CO A:CO504 3.0 18.1 1.0
CD A:GLU280 3.1 9.5 1.0
CD A:GLU187 3.1 21.1 1.0
CD2 A:HIS153 3.2 15.3 1.0
CG A:ASP93 3.2 12.6 1.0
CE1 A:HIS153 3.3 15.9 1.0
OE1 A:GLU280 3.4 15.1 1.0
OE1 A:GLU187 3.5 25.4 1.0
OD1 A:ASP93 3.7 17.5 1.0
O A:HOH520 3.9 22.0 1.0
CB A:ALA185 4.0 14.9 1.0
CG A:GLU187 4.2 22.3 1.0
CG A:HIS153 4.4 15.1 1.0
CB A:ASP93 4.4 16.4 1.0
ND1 A:HIS153 4.4 17.1 1.0
CG A:GLU280 4.4 13.8 1.0
CB A:GLU187 4.5 17.2 1.0
OD1 A:ASP82 4.6 14.9 1.0

Cobalt binding site 3 out of 6 in 2dfi

Go back to Cobalt Binding Sites List in 2dfi
Cobalt binding site 3 out of 6 in the Crystal Structure of Pf-Map(1-292)-C


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Pf-Map(1-292)-C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co506

b:28.1
occ:1.00
 NE2 B:HIS173 2.3 26.5 1.0
NE2 A:HIS62 2.3 17.7 1.0
CE1 B:HIS173 2.6 28.4 1.0
CD2 A:HIS62 3.0 16.5 1.0
CE1 A:HIS62 3.5 19.6 1.0
CD2 B:HIS173 3.6 27.0 1.0
ND1 B:HIS173 3.8 28.6 1.0
O A:HOH520 4.2 22.0 1.0
CE1 A:HIS161 4.2 27.5 1.0
CG A:HIS62 4.3 17.3 1.0
CG B:HIS173 4.3 26.3 1.0
ND1 A:HIS62 4.4 16.3 1.0
NE2 A:HIS161 4.4 27.6 1.0

Cobalt binding site 4 out of 6 in 2dfi

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Cobalt binding site 4 out of 6 in the Crystal Structure of Pf-Map(1-292)-C


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Pf-Map(1-292)-C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co501

b:19.3
occ:1.00
 OE1 B:GLU280 2.0 16.9 1.0
OD1 B:ASP93 2.1 19.3 1.0
OD2 B:ASP82 2.1 12.9 1.0
OD1 B:ASP82 2.5 13.4 1.0
CG B:ASP82 2.6 16.3 1.0
CG B:ASP93 2.8 19.0 1.0
CD B:GLU280 2.8 17.4 1.0
OD2 B:ASP93 2.9 17.6 1.0
CO B:CO502 3.0 17.1 1.0
OE2 B:GLU280 3.0 16.5 1.0
O B:HOH593 3.8 34.3 1.0
CZ B:PHE50 4.0 12.9 1.0
OE1 B:GLU187 4.1 21.8 1.0
CD B:GLU187 4.1 19.3 1.0
CB B:ASP82 4.1 14.0 1.0
OE2 B:GLU187 4.2 15.7 1.0
CG B:GLU280 4.3 17.7 1.0
CB B:ASP93 4.3 17.0 1.0
O B:THR94 4.3 17.3 1.0
N B:THR94 4.5 15.9 1.0
NE2 B:GLN278 4.6 16.0 1.0
C B:ASP93 4.6 16.7 1.0
C B:THR94 4.6 17.1 1.0
CB B:ALA95 4.6 16.3 1.0
CE1 B:PHE50 4.7 16.9 1.0
CE2 B:PHE50 4.8 16.0 1.0
CA B:ASP93 4.8 18.0 1.0
CG B:GLU187 4.8 21.4 1.0
CA B:ASP82 4.9 15.8 1.0
CB B:GLU280 4.9 15.5 1.0
O B:HOH604 4.9 27.0 1.0
CA B:THR94 5.0 16.9 1.0

Cobalt binding site 5 out of 6 in 2dfi

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Cobalt binding site 5 out of 6 in the Crystal Structure of Pf-Map(1-292)-C


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Pf-Map(1-292)-C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co502

b:17.1
occ:1.00
 OD2 B:ASP93 2.0 17.6 1.0
OE2 B:GLU280 2.1 16.5 1.0
OE2 B:GLU187 2.2 15.7 1.0
NE2 B:HIS153 2.3 9.9 1.0
CD B:GLU187 2.9 19.3 1.0
CO B:CO501 3.0 19.3 1.0
CG B:ASP93 3.1 19.0 1.0
CD B:GLU280 3.2 17.4 1.0
CD2 B:HIS153 3.2 11.5 1.0
CE1 B:HIS153 3.2 14.1 1.0
OE1 B:GLU280 3.6 16.9 1.0
OD1 B:ASP93 3.6 19.3 1.0
OE1 B:GLU187 3.6 21.8 1.0
CG B:GLU187 3.7 21.4 1.0
O B:HOH604 3.8 27.0 1.0
CB B:ALA185 4.0 16.6 1.0
O B:HOH505 4.0 18.4 1.0
CB B:ASP93 4.3 17.0 1.0
ND1 B:HIS153 4.4 12.9 1.0
O B:HOH593 4.4 34.3 1.0
CG B:HIS153 4.4 12.8 1.0
CG B:GLU280 4.5 17.7 1.0
OD1 B:ASP82 4.8 13.4 1.0

Cobalt binding site 6 out of 6 in 2dfi

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Cobalt binding site 6 out of 6 in the Crystal Structure of Pf-Map(1-292)-C


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of Pf-Map(1-292)-C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co503

b:28.6
occ:1.00
 NE2 A:HIS173 2.2 26.3 1.0
O B:HOH651 2.3 38.6 1.0
NE2 B:HIS62 2.4 17.0 1.0
O B:HOH604 2.4 27.0 1.0
CE1 A:HIS173 2.6 27.6 1.0
CD2 B:HIS62 3.1 16.5 1.0
CD2 A:HIS173 3.5 26.2 1.0
CE1 B:HIS62 3.5 17.3 1.0
ND1 A:HIS173 3.9 28.5 1.0
O B:HOH505 4.1 18.4 1.0
O B:HOH582 4.1 42.5 1.0
O B:HOH593 4.1 34.3 1.0
CG A:HIS173 4.3 25.3 1.0
CG B:HIS62 4.3 16.1 1.0
CE1 B:HIS161 4.4 24.5 1.0
ND1 B:HIS62 4.5 14.5 1.0
NE2 B:HIS161 4.6 25.7 1.0
O B:HOH542 4.7 24.2 1.0

Reference:

K.Takano, Y.Katagiri, A.Mukaiyama, H.Chon, H.Matsumura, Y.Koga, S.Kanaya. Conformational Contagion in A Protein: Structural Properties of A Chameleon Sequence Proteins V. 68 617 2007.
ISSN: ISSN 0887-3585
PubMed: 17510955
DOI: 10.1002/PROT.21451
Page generated: Sun Jul 13 18:06:37 2025

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