Atomistry » Cobalt » PDB 1zfv-2dfi » 2dfi
Atomistry »
  Cobalt »
    PDB 1zfv-2dfi »
      2dfi »

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

Go back to Cobalt Binding Sites List in 2dfi
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

Go back to Cobalt Binding Sites List in 2dfi
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

Go back to Cobalt Binding Sites List in 2dfi
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

Go back to Cobalt Binding Sites List in 2dfi
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: Tue Jul 30 15:00:57 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy