Atomistry » Cobalt » PDB 4ngo-4rum » 4njq
Atomistry »
  Cobalt »
    PDB 4ngo-4rum »
      4njq »

Cobalt in PDB 4njq: Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa

Protein crystallography data

The structure of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa, PDB code: 4njq was solved by D.D.Nguyen, R.Pandian, D.Y.Kim, S.C.Ha, K.H.Yun, K.S.Kim, J.H.Kim, K.K.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.76 / 2.70
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 133.205, 133.205, 322.316, 90.00, 90.00, 120.00
R / Rfree (%) 16.7 / 22.3

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa (pdb code 4njq). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa, PDB code: 4njq:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 4njq

Go back to Cobalt Binding Sites List in 4njq
Cobalt binding site 1 out of 8 in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co501

b:35.9
occ:1.00
OD1 A:ASP236 2.1 39.1 1.0
OD2 A:ASP307 2.1 30.0 1.0
NE2 A:HIS82 2.2 30.2 1.0
OD1 A:ASP307 2.3 34.7 1.0
CG A:ASP307 2.5 33.7 1.0
O3 A:CO3503 2.7 49.7 1.0
CG A:ASP236 2.9 38.2 1.0
CE1 A:HIS82 3.1 31.6 1.0
OD2 A:ASP236 3.2 41.0 1.0
CO A:CO502 3.3 39.5 1.0
CD2 A:HIS82 3.3 35.2 1.0
C A:CO3503 3.5 54.9 1.0
O2 A:CO3503 3.7 44.9 1.0
CB A:ASP307 4.0 27.9 1.0
CB A:ASN237 4.0 33.1 1.0
OE1 A:GLU266 4.2 37.0 1.0
ND1 A:HIS82 4.2 33.8 1.0
CB A:ASP236 4.3 35.2 1.0
CG A:ASN237 4.3 32.3 1.0
CG A:HIS82 4.4 36.5 1.0
OD1 A:ASN237 4.6 33.5 1.0
OE2 A:GLU266 4.7 45.5 1.0
OE1 A:GLU265 4.7 62.6 1.0
O1 A:CO3503 4.7 51.1 1.0
CA A:ASP236 4.8 34.6 1.0
CA A:ASP307 4.8 33.5 1.0
ND2 A:ASN237 4.8 32.3 1.0
CD A:GLU266 4.8 41.3 1.0
N A:ASN308 4.8 32.8 1.0
C A:ASP236 4.9 33.6 1.0
CA A:ASN237 5.0 34.4 1.0

Cobalt binding site 2 out of 8 in 4njq

Go back to Cobalt Binding Sites List in 4njq
Cobalt binding site 2 out of 8 in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co502

b:39.5
occ:1.00
O2 A:CO3503 1.7 44.9 1.0
OD2 A:ASP236 1.9 41.0 1.0
OE2 A:GLU266 2.3 45.5 1.0
OE1 A:GLU266 2.4 37.0 1.0
CD2 A:HIS401 2.6 41.8 1.0
C A:CO3503 2.6 54.9 1.0
CD A:GLU266 2.6 41.3 1.0
NE2 A:HIS401 2.7 40.6 1.0
O3 A:CO3503 2.9 49.7 1.0
CG A:ASP236 2.9 38.2 1.0
OD1 A:ASP236 3.3 39.1 1.0
CO A:CO501 3.3 35.9 1.0
O1 A:CO3503 3.8 51.1 1.0
CG A:HIS401 3.9 44.7 1.0
CE1 A:HIS401 4.0 36.1 1.0
CG A:GLU266 4.1 43.8 1.0
CB A:ASP236 4.2 35.2 1.0
CE1 A:HIS82 4.3 31.6 1.0
NE2 A:HIS82 4.5 30.2 1.0
NE2 D:HIS156 4.5 43.3 1.0
CD A:PRO86 4.5 33.6 1.0
ND1 A:HIS401 4.6 39.8 1.0
CE1 D:HIS156 4.7 40.8 1.0
SD A:MET400 4.9 47.7 1.0
CG A:PRO86 4.9 32.9 1.0
CB A:HIS401 5.0 44.9 1.0

Cobalt binding site 3 out of 8 in 4njq

Go back to Cobalt Binding Sites List in 4njq
Cobalt binding site 3 out of 8 in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co501

b:36.0
occ:1.00
OD1 B:ASP236 2.1 37.6 1.0
OD1 B:ASP307 2.1 33.4 1.0
NE2 B:HIS82 2.2 36.1 1.0
OD2 B:ASP307 2.6 41.7 1.0
O1 B:CO3503 2.6 45.9 1.0
CG B:ASP307 2.7 34.4 1.0
CE1 B:HIS82 2.8 32.9 1.0
CG B:ASP236 3.1 36.6 1.0
O2 B:CO3503 3.2 45.0 1.0
CO B:CO502 3.3 40.1 1.0
C B:CO3503 3.3 52.8 1.0
OD2 B:ASP236 3.4 40.6 1.0
CD2 B:HIS82 3.4 41.7 1.0
CE B:MET400 3.8 50.4 1.0
ND1 B:HIS82 4.0 32.0 1.0
CB B:ASN237 4.1 32.9 1.0
CB B:ASP307 4.1 30.3 1.0
OE1 B:GLU265 4.3 61.9 1.0
OE2 B:GLU266 4.3 43.9 1.0
OE1 B:GLU266 4.3 49.4 1.0
CG B:HIS82 4.4 36.5 1.0
CB B:ASP236 4.4 35.2 1.0
CG B:ASN237 4.4 34.1 1.0
O3 B:CO3503 4.5 55.5 1.0
CD B:GLU266 4.7 46.8 1.0
ND2 B:ASN237 4.8 35.8 1.0
OD1 B:ASN237 4.8 29.8 1.0
CA B:ASP307 4.8 35.8 1.0
CA B:ASP236 4.9 32.0 1.0
N B:ASN308 4.9 36.4 1.0
CA B:ASN237 5.0 29.3 1.0
C B:ASP236 5.0 37.2 1.0

Cobalt binding site 4 out of 8 in 4njq

Go back to Cobalt Binding Sites List in 4njq
Cobalt binding site 4 out of 8 in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co502

b:40.1
occ:1.00
O2 B:CO3503 1.8 45.0 1.0
OE1 B:GLU266 1.8 49.4 1.0
OD2 B:ASP236 1.9 40.6 1.0
NE2 B:HIS401 2.2 40.4 1.0
CD B:GLU266 2.5 46.8 1.0
OE2 B:GLU266 2.6 43.9 1.0
C B:CO3503 2.6 52.8 1.0
CG B:ASP236 2.9 36.6 1.0
O1 B:CO3503 3.0 45.9 1.0
CD2 B:HIS401 3.0 36.9 1.0
OD1 B:ASP236 3.2 37.6 1.0
CO B:CO501 3.3 36.0 1.0
CE1 B:HIS401 3.3 38.4 1.0
O3 B:CO3503 3.7 55.5 1.0
CG B:GLU266 3.9 46.6 1.0
CE B:MET400 4.1 50.4 1.0
CG B:HIS401 4.2 38.0 1.0
CB B:ASP236 4.3 35.2 1.0
CE1 B:HIS82 4.3 32.9 1.0
ND1 B:HIS401 4.3 35.4 1.0
CD B:PRO86 4.5 33.2 1.0
NE2 B:HIS82 4.6 36.1 1.0
CG B:PRO86 4.7 30.2 1.0
CG B:MET400 4.8 41.1 1.0
CB B:GLU266 5.0 40.1 1.0

Cobalt binding site 5 out of 8 in 4njq

Go back to Cobalt Binding Sites List in 4njq
Cobalt binding site 5 out of 8 in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co501

b:37.7
occ:1.00
OD1 C:ASP236 2.0 36.3 1.0
OD1 C:ASP307 2.2 41.1 1.0
NE2 C:HIS82 2.3 34.2 1.0
O2 C:CO3503 2.4 46.8 1.0
OD2 C:ASP307 2.4 42.6 1.0
CG C:ASP307 2.6 37.5 1.0
CG C:ASP236 2.9 35.9 1.0
CE1 C:HIS82 3.1 34.7 1.0
OD2 C:ASP236 3.2 35.1 1.0
CD2 C:HIS82 3.3 37.5 1.0
CO C:CO502 3.3 40.0 1.0
C C:CO3503 3.4 56.0 1.0
O C:HOH624 3.4 50.4 1.0
O3 C:CO3503 3.8 45.9 1.0
CB C:ASN237 4.1 34.4 1.0
CB C:ASP307 4.1 33.9 1.0
OE1 C:GLU266 4.3 39.0 1.0
CB C:ASP236 4.3 32.6 1.0
ND1 C:HIS82 4.3 36.6 1.0
O1 C:CO3503 4.3 61.1 1.0
CG C:ASN237 4.4 38.2 1.0
CG C:HIS82 4.4 37.8 1.0
OE2 C:GLU266 4.5 44.6 1.0
OE1 C:GLU265 4.6 65.9 1.0
ND2 C:ASN237 4.7 34.9 1.0
CE C:MET400 4.8 45.2 1.0
CD C:GLU266 4.8 44.8 1.0
OD1 C:ASN237 4.8 37.1 1.0
CA C:ASP236 4.8 32.8 1.0
N C:ASN308 4.8 36.0 1.0
CA C:ASP307 4.9 35.5 1.0
C C:ASP236 4.9 36.5 1.0
CA C:ASN237 4.9 30.3 1.0
N C:ASN237 5.0 35.1 1.0

Cobalt binding site 6 out of 8 in 4njq

Go back to Cobalt Binding Sites List in 4njq
Cobalt binding site 6 out of 8 in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co502

b:40.0
occ:1.00
OD2 C:ASP236 1.9 35.1 1.0
NE2 C:HIS401 2.1 41.2 1.0
OE2 C:GLU266 2.2 44.6 1.0
OE1 C:GLU266 2.4 39.0 1.0
O3 C:CO3503 2.5 45.9 1.0
CD C:GLU266 2.5 44.8 1.0
O2 C:CO3503 2.7 46.8 1.0
C C:CO3503 2.9 56.0 1.0
CG C:ASP236 3.0 35.9 1.0
CD2 C:HIS401 3.0 37.3 1.0
CE1 C:HIS401 3.1 36.0 1.0
CO C:CO501 3.3 37.7 1.0
OD1 C:ASP236 3.4 36.3 1.0
CG C:GLU266 4.0 41.3 1.0
CG C:HIS401 4.1 37.6 1.0
ND1 C:HIS401 4.1 31.1 1.0
O1 C:CO3503 4.2 61.1 1.0
CE C:MET400 4.2 45.2 1.0
CB C:ASP236 4.3 32.6 1.0
CD C:PRO86 4.4 36.6 1.0
CE1 C:HIS82 4.5 34.7 1.0
NE2 C:HIS82 4.5 34.2 1.0
CG C:PRO86 4.6 31.1 1.0
O C:HOH624 4.8 50.4 1.0
CG C:MET400 5.0 35.8 1.0
CB C:GLU266 5.0 39.3 1.0

Cobalt binding site 7 out of 8 in 4njq

Go back to Cobalt Binding Sites List in 4njq
Cobalt binding site 7 out of 8 in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co501

b:39.0
occ:1.00
OE2 D:GLU266 1.8 40.1 1.0
OD2 D:ASP236 2.0 32.0 1.0
NE2 D:HIS401 2.2 34.7 1.0
O2 D:CO3503 2.5 46.8 1.0
CD D:GLU266 2.6 38.7 1.0
O3 D:CO3503 2.7 55.8 1.0
OE1 D:GLU266 2.8 44.3 1.0
C D:CO3503 2.9 55.3 1.0
CG D:ASP236 3.0 36.9 1.0
CD2 D:HIS401 3.1 36.1 1.0
CE1 D:HIS401 3.3 35.2 1.0
CO D:CO502 3.3 37.0 1.0
OD1 D:ASP236 3.4 38.7 1.0
CE D:MET400 3.8 47.4 1.0
CG D:GLU266 4.0 33.4 1.0
O1 D:CO3503 4.2 60.2 1.0
NE2 A:HIS156 4.2 41.5 1.0
CG D:HIS401 4.3 37.9 1.0
ND1 D:HIS401 4.3 38.4 1.0
CB D:ASP236 4.3 34.9 1.0
CE1 D:HIS82 4.5 33.1 1.0
CE1 A:HIS156 4.6 36.8 1.0
NE2 D:HIS82 4.6 36.1 1.0
CD D:PRO86 4.6 31.7 1.0
CG D:PRO86 4.8 31.4 1.0
CG D:MET400 4.8 33.4 1.0

Cobalt binding site 8 out of 8 in 4njq

Go back to Cobalt Binding Sites List in 4njq
Cobalt binding site 8 out of 8 in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co502

b:37.0
occ:1.00
OD1 D:ASP236 2.1 38.7 1.0
O3 D:CO3503 2.1 55.8 1.0
OD1 D:ASP307 2.1 34.8 1.0
NE2 D:HIS82 2.2 36.1 1.0
OD2 D:ASP307 2.6 37.0 1.0
CG D:ASP307 2.7 36.2 1.0
CG D:ASP236 3.0 36.9 1.0
CE1 D:HIS82 3.1 33.1 1.0
OD2 D:ASP236 3.3 32.0 1.0
CO D:CO501 3.3 39.0 1.0
CD2 D:HIS82 3.4 33.6 1.0
C D:CO3503 3.4 55.3 1.0
OE2 D:GLU266 3.7 40.1 1.0
CE D:MET400 3.9 47.4 1.0
CB D:ASN237 4.1 33.5 1.0
CB D:ASP307 4.2 30.1 1.0
O2 D:CO3503 4.2 46.8 1.0
ND1 D:HIS82 4.2 31.5 1.0
O1 D:CO3503 4.3 60.2 1.0
CB D:ASP236 4.3 34.9 1.0
CG D:ASN237 4.4 37.7 1.0
CG D:HIS82 4.4 31.2 1.0
ND2 D:ASN237 4.7 32.3 1.0
CD D:GLU266 4.7 38.7 1.0
CA D:ASP236 4.8 31.7 1.0
CA D:ASP307 4.9 32.4 1.0
N D:ASN308 4.9 39.3 1.0
OD1 D:ASN237 4.9 38.0 1.0

Reference:

D.D.Nguyen, R.Pandian, D.Kim, S.C.Ha, H.J.Yoon, K.S.Kim, K.H.Yun, J.H.Kim, K.K.Kim. Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa Biochem.Biophys.Res.Commun. V. 447 101 2014.
ISSN: ISSN 0006-291X
PubMed: 24704201
DOI: 10.1016/J.BBRC.2014.03.109
Page generated: Tue Jul 30 17:23:22 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy