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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

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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

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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

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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

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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

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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

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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

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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

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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: Sun Dec 13 10:45:22 2020

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