Zinc in PDB 6xbe: Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F

Protein crystallography data

The structure of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F, PDB code: 6xbe was solved by L.J.Worrall, T.Sun, V.K.Mulligan, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.76 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 42.699, 74.551, 77.31, 96.52, 103.11, 106.24
R / Rfree (%) 18.5 / 22.3

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F (pdb code 6xbe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F, PDB code: 6xbe:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 6xbe

Go back to Zinc Binding Sites List in 6xbe
Zinc binding site 1 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:25.5
occ:1.00
ND1 A:HIS122 2.0 23.7 1.0
NE2 A:HIS189 2.1 28.6 1.0
NE2 A:HIS120 2.2 25.9 1.0
SG F:DCY1004 2.3 29.4 1.0
CE1 A:HIS122 3.0 24.9 1.0
CG A:HIS122 3.1 24.3 1.0
CD2 A:HIS189 3.1 25.6 1.0
CD2 A:HIS120 3.1 23.4 1.0
CE1 A:HIS189 3.1 24.7 1.0
CE1 A:HIS120 3.1 26.6 1.0
CB F:DCY1004 3.2 29.0 1.0
CB A:HIS122 3.4 24.1 1.0
ZN A:ZN302 3.8 20.8 1.0
OD1 A:ASP124 4.1 26.2 1.0
NE2 A:HIS122 4.1 25.2 1.0
SG A:CYS208 4.1 25.6 1.0
CD2 A:HIS122 4.2 23.7 1.0
ND1 A:HIS189 4.2 25.4 1.0
ND1 A:HIS120 4.2 24.1 1.0
CG A:HIS120 4.2 24.1 1.0
CG A:HIS189 4.2 25.4 1.0
CB A:CYS208 4.3 24.5 1.0
CG2 A:THR190 4.6 25.2 1.0
OD2 A:ASP124 4.6 33.5 1.0
CA F:DCY1004 4.7 28.3 1.0
CG A:ASP124 4.8 29.2 1.0
O A:HOH528 4.8 29.3 1.0
CA A:HIS122 4.8 23.1 1.0

Zinc binding site 2 out of 12 in 6xbe

Go back to Zinc Binding Sites List in 6xbe
Zinc binding site 2 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:20.8
occ:1.00
OD2 A:ASP124 2.0 33.5 1.0
NE2 A:HIS250 2.2 27.7 1.0
SG F:DCY1004 2.3 29.4 1.0
SG A:CYS208 2.3 25.6 1.0
O A:HOH528 3.1 29.3 1.0
CG A:ASP124 3.1 29.2 1.0
CD2 A:HIS250 3.2 29.7 1.0
CE1 A:HIS250 3.2 26.3 1.0
CB A:CYS208 3.4 24.5 1.0
CB F:DCY1004 3.5 29.0 1.0
OD1 A:ASP124 3.6 26.2 1.0
ZN A:ZN301 3.8 25.5 1.0
CA F:DCY1004 4.0 28.3 1.0
CD F:PRO1005 4.1 35.0 1.0
ND1 A:HIS250 4.3 27.0 1.0
CB A:SER249 4.3 24.3 1.0
CG A:HIS250 4.3 30.1 1.0
CB A:ASP124 4.3 27.5 1.0
N F:PRO1005 4.4 34.2 1.0
NE2 A:HIS189 4.4 28.6 1.0
C F:DCY1004 4.4 33.7 1.0
CA A:CYS208 4.6 26.1 1.0
CE1 A:HIS189 4.6 24.7 1.0
CE1 A:HIS120 4.6 26.6 1.0
NE2 A:HIS120 4.6 25.9 1.0
OG A:SER249 4.7 28.0 1.0
O A:HOH407 4.9 44.1 1.0

Zinc binding site 3 out of 12 in 6xbe

Go back to Zinc Binding Sites List in 6xbe
Zinc binding site 3 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:45.8
occ:1.00
O F:HOH1104 2.2 43.8 1.0
O A:HOH489 2.3 32.6 1.0
OE2 A:GLU152 2.6 40.4 1.0
OE1 A:GLU152 2.6 34.4 1.0
CD A:GLU152 3.0 36.5 1.0
NH2 F:DAR1002 3.8 52.0 1.0
NE F:DAR1002 3.9 54.4 1.0
NE2 A:HIS122 4.0 25.2 1.0
O A:HOH532 4.3 32.1 1.0
CZ F:DAR1002 4.3 56.8 1.0
CG A:GLU152 4.5 33.8 1.0
CD2 A:HIS122 4.6 23.7 1.0
O A:HOH417 4.8 41.5 1.0
CB A:ASP223 5.0 50.0 1.0

Zinc binding site 4 out of 12 in 6xbe

Go back to Zinc Binding Sites List in 6xbe
Zinc binding site 4 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:28.9
occ:1.00
NE2 B:HIS189 2.0 27.5 1.0
ND1 B:HIS122 2.1 25.3 1.0
NE2 B:HIS120 2.1 25.1 1.0
SG G:DCY1004 2.3 35.9 1.0
CD2 B:HIS189 3.0 25.3 1.0
CE1 B:HIS122 3.0 27.6 1.0
CD2 B:HIS120 3.0 25.6 1.0
CE1 B:HIS189 3.1 27.2 1.0
CE1 B:HIS120 3.1 26.4 1.0
CG B:HIS122 3.1 25.1 1.0
CB G:DCY1004 3.3 38.7 1.0
CB B:HIS122 3.4 24.2 1.0
ZN B:ZN302 3.8 22.9 1.0
OD1 B:ASP124 4.1 26.7 1.0
SG B:CYS208 4.1 32.4 1.0
CG B:HIS189 4.1 26.8 1.0
ND1 B:HIS120 4.1 25.6 1.0
ND1 B:HIS189 4.2 28.0 1.0
CG B:HIS120 4.2 25.8 1.0
NE2 B:HIS122 4.2 27.2 1.0
CD2 B:HIS122 4.2 29.1 1.0
CB B:CYS208 4.2 30.3 1.0
O B:HOH498 4.4 32.6 1.0
CG2 B:THR190 4.6 27.6 1.0
OD2 B:ASP124 4.6 30.3 1.0
CA G:DCY1004 4.7 39.0 1.0
CG B:ASP124 4.8 31.6 1.0
CA B:HIS122 4.9 24.5 1.0
O B:HOH412 5.0 35.4 1.0

Zinc binding site 5 out of 12 in 6xbe

Go back to Zinc Binding Sites List in 6xbe
Zinc binding site 5 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:22.9
occ:1.00
OD2 B:ASP124 2.0 30.3 1.0
NE2 B:HIS250 2.2 33.2 1.0
SG G:DCY1004 2.3 35.9 1.0
SG B:CYS208 2.3 32.4 1.0
O B:HOH498 2.5 32.6 1.0
CG B:ASP124 3.1 31.6 1.0
CD2 B:HIS250 3.1 30.3 1.0
CE1 B:HIS250 3.2 31.4 1.0
CB B:CYS208 3.4 30.3 1.0
CB G:DCY1004 3.5 38.7 1.0
OD1 B:ASP124 3.6 26.7 1.0
ZN B:ZN301 3.8 28.9 1.0
CA G:DCY1004 3.9 39.0 1.0
CD G:PRO1005 4.0 45.0 1.0
ND1 B:HIS250 4.3 33.0 1.0
CG B:HIS250 4.3 32.1 1.0
N G:PRO1005 4.3 43.1 1.0
CB B:SER249 4.3 27.7 1.0
C G:DCY1004 4.3 44.4 1.0
CB B:ASP124 4.4 30.3 1.0
NE2 B:HIS189 4.4 27.5 1.0
CA B:CYS208 4.5 29.2 1.0
CE1 B:HIS189 4.6 27.2 1.0
CE1 B:HIS120 4.6 26.4 1.0
NE2 B:HIS120 4.7 25.1 1.0
OG B:SER249 4.7 28.7 1.0

Zinc binding site 6 out of 12 in 6xbe

Go back to Zinc Binding Sites List in 6xbe
Zinc binding site 6 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:21.1
occ:1.00
OD2 B:ASP223 2.2 37.9 1.0
OE2 C:GLU227 2.2 41.9 1.0
OE2 B:GLU152 2.3 26.1 1.0
O B:HOH508 2.3 23.3 1.0
OE1 B:GLU152 2.4 27.9 1.0
OE1 C:GLU227 2.4 38.6 1.0
CD C:GLU227 2.6 37.2 1.0
CD B:GLU152 2.7 24.1 1.0
OD1 B:ASP223 2.8 47.2 1.0
CG B:ASP223 2.8 41.6 1.0
O B:HOH463 4.1 33.9 1.0
CG C:GLU227 4.2 39.1 1.0
NE2 B:HIS122 4.2 27.2 1.0
CG B:GLU152 4.2 25.4 1.0
CB B:ASP223 4.3 39.8 1.0
NE2 C:HIS228 4.4 36.0 1.0
O B:HOH431 4.5 36.5 1.0
O G:HOH1102 4.5 52.4 1.0
CE1 C:HIS228 4.6 37.8 1.0
CD2 B:HIS122 4.7 29.1 1.0
O C:HOH457 4.8 38.0 1.0

Zinc binding site 7 out of 12 in 6xbe

Go back to Zinc Binding Sites List in 6xbe
Zinc binding site 7 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:36.1
occ:1.00
OE2 B:GLU227 2.0 46.0 1.0
O C:HOH460 2.4 34.9 1.0
OD2 C:ASP223 2.4 49.4 1.0
OE2 C:GLU152 2.4 42.5 1.0
OE1 C:GLU152 2.5 45.8 1.0
OE1 B:GLU227 2.6 52.1 1.0
CD B:GLU227 2.6 49.3 1.0
CD C:GLU152 2.7 46.9 1.0
OD1 C:ASP223 2.9 51.1 1.0
CG C:ASP223 3.0 51.6 1.0
NE2 C:HIS122 4.0 30.5 1.0
CG B:GLU227 4.1 42.4 1.0
CG C:GLU152 4.3 42.2 1.0
O C:HOH429 4.3 36.5 1.0
NE2 B:HIS228 4.4 37.8 1.0
CE1 B:HIS228 4.5 38.2 1.0
CB C:ASP223 4.5 46.6 1.0
CD2 C:HIS122 4.6 32.3 1.0
CD H:DAR1002 4.8 49.5 1.0
O H:HOH1101 4.8 24.3 0.5
CB B:GLU227 4.9 37.8 1.0
O B:HOH475 4.9 43.4 1.0

Zinc binding site 8 out of 12 in 6xbe

Go back to Zinc Binding Sites List in 6xbe
Zinc binding site 8 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:34.5
occ:1.00
ND1 C:HIS122 2.1 35.8 1.0
NE2 C:HIS189 2.1 31.2 1.0
NE2 C:HIS120 2.1 30.2 1.0
SG H:DCY1004 2.4 45.8 1.0
CD2 C:HIS189 3.0 30.9 1.0
CE1 C:HIS122 3.0 33.0 1.0
CD2 C:HIS120 3.0 35.5 1.0
CE1 C:HIS120 3.0 34.7 1.0
CG C:HIS122 3.1 33.8 1.0
CE1 C:HIS189 3.1 30.1 1.0
CB H:DCY1004 3.3 44.3 1.0
CB C:HIS122 3.4 34.7 1.0
ZN C:ZN302 3.8 30.5 1.0
OD1 C:ASP124 4.1 35.4 1.0
SG C:CYS208 4.1 30.4 1.0
O C:HOH447 4.1 53.6 1.0
ND1 C:HIS120 4.1 36.6 1.0
NE2 C:HIS122 4.1 30.5 1.0
CG C:HIS120 4.1 32.6 1.0
CG C:HIS189 4.2 28.9 1.0
CD2 C:HIS122 4.2 32.3 1.0
ND1 C:HIS189 4.2 28.6 1.0
CB C:CYS208 4.2 32.6 1.0
CG2 C:THR190 4.6 33.1 1.0
OD2 C:ASP124 4.6 32.2 1.0
CA H:DCY1004 4.7 44.3 1.0
CG C:ASP124 4.8 37.3 1.0
O C:HOH417 4.8 42.5 1.0
CA C:HIS122 4.9 34.4 1.0

Zinc binding site 9 out of 12 in 6xbe

Go back to Zinc Binding Sites List in 6xbe
Zinc binding site 9 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:30.5
occ:1.00
OD2 C:ASP124 1.9 32.2 1.0
NE2 C:HIS250 2.1 37.4 1.0
SG C:CYS208 2.3 30.4 1.0
SG H:DCY1004 2.3 45.8 1.0
O C:HOH447 2.4 53.6 1.0
CG C:ASP124 3.0 37.3 1.0
CE1 C:HIS250 3.0 35.8 1.0
CD2 C:HIS250 3.1 37.9 1.0
CB C:CYS208 3.4 32.6 1.0
OD1 C:ASP124 3.5 35.4 1.0
CB H:DCY1004 3.5 44.3 1.0
ZN C:ZN301 3.8 34.5 1.0
CA H:DCY1004 4.0 44.3 1.0
CB C:SER249 4.1 37.7 1.0
ND1 C:HIS250 4.2 38.3 1.0
CD H:PRO1005 4.2 42.2 1.0
CG C:HIS250 4.2 38.2 1.0
CB C:ASP124 4.2 35.8 1.0
NE2 C:HIS189 4.5 31.2 1.0
CE1 C:HIS120 4.5 34.7 1.0
N H:PRO1005 4.5 40.3 1.0
OG C:SER249 4.5 37.5 1.0
C H:DCY1004 4.5 41.8 1.0
CA C:CYS208 4.6 30.0 1.0
NE2 C:HIS120 4.6 30.2 1.0
CE1 C:HIS189 4.8 30.1 1.0
CE C:LYS125 4.9 37.5 1.0

Zinc binding site 10 out of 12 in 6xbe

Go back to Zinc Binding Sites List in 6xbe
Zinc binding site 10 out of 12 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-1F within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:33.3
occ:1.00
ND1 D:HIS122 2.0 25.8 1.0
NE2 D:HIS189 2.1 30.7 1.0
NE2 D:HIS120 2.1 26.6 1.0
SG I:DCY1004 2.5 47.7 1.0
CE1 D:HIS122 2.9 31.0 1.0
CG D:HIS122 3.0 28.6 1.0
CD2 D:HIS189 3.0 29.6 1.0
CD2 D:HIS120 3.0 26.4 1.0
CE1 D:HIS120 3.1 27.3 1.0
CE1 D:HIS189 3.2 31.0 1.0
CB D:HIS122 3.4 32.9 1.0
CB I:DCY1004 3.4 49.3 1.0
ZN D:ZN302 3.8 27.7 1.0
NE2 D:HIS122 4.0 31.4 1.0
CD2 D:HIS122 4.1 29.1 1.0
OD1 D:ASP124 4.1 39.2 1.0
CG D:HIS120 4.2 26.7 1.0
ND1 D:HIS120 4.2 26.7 1.0
SG D:CYS208 4.2 38.6 1.0
CG D:HIS189 4.2 29.1 1.0
ND1 D:HIS189 4.2 27.7 1.0
CB D:CYS208 4.3 31.2 1.0
CG2 D:THR190 4.5 29.3 1.0
OD2 D:ASP124 4.6 35.9 1.0
O D:HOH477 4.7 28.9 1.0
CG D:ASP124 4.8 37.8 1.0
CA D:HIS122 4.8 32.7 1.0
CA I:DCY1004 4.9 53.9 1.0

Reference:

V.K.Mulligan, S.Workman, T.Sun, S.Rettie, X.Li, L.J.Worrall, T.W.Craven, D.T.King, P.Hosseinzadeh, A.M.Watkins, P.D.Renfrew, S.Guffy, J.W.Labonte, R.Moretti, R.Bonneau, N.C.J.Strynadka, D.Baker. Computationally Designed Peptide Macrocycle Inhibitors of New Delhi Metallo-Beta-Lactamase 1. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 33723038
DOI: 10.1073/PNAS.2012800118
Page generated: Sat Apr 3 18:27:50 2021

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy