Zinc in PDB 6j4n: Structure of Papua New Guinea Mbl-1(Pngm-1) Native

Protein crystallography data

The structure of Structure of Papua New Guinea Mbl-1(Pngm-1) Native, PDB code: 6j4n was solved by M.K.Hong, K.S.Park, J.H.Jeon, J.H.Lee, Y.S.Park, S.H.Lee, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.39 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 122.274, 83.017, 163.469, 90.00, 110.55, 90.00
R / Rfree (%) 19 / 24.4

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Structure of Papua New Guinea Mbl-1(Pngm-1) Native (pdb code 6j4n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Structure of Papua New Guinea Mbl-1(Pngm-1) Native, PDB code: 6j4n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 6j4n

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Zinc binding site 1 out of 16 in the Structure of Papua New Guinea Mbl-1(Pngm-1) Native


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Papua New Guinea Mbl-1(Pngm-1) Native within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:25.9
occ:1.00
O A:HOH520 2.1 20.3 1.0
OD2 A:ASP210 2.2 12.9 1.0
NE2 A:HIS279 2.3 16.9 1.0
NE2 A:HIS96 2.4 11.3 1.0
OD1 A:ASP95 2.4 14.7 1.0
CD2 A:HIS96 2.9 11.1 1.0
O A:HOH672 2.9 34.2 1.0
CG A:ASP210 3.0 13.9 1.0
ZN A:ZN402 3.1 20.7 1.0
CE1 A:HIS279 3.2 18.9 1.0
OD1 A:ASP210 3.2 15.8 1.0
CD2 A:HIS279 3.3 16.9 1.0
CG A:ASP95 3.3 14.2 1.0
OD2 A:ASP95 3.6 14.3 1.0
CE1 A:HIS96 3.6 11.8 1.0
NE2 A:HIS91 3.9 10.9 1.0
O A:HOH656 4.1 31.6 1.0
O A:HOH584 4.1 24.1 1.0
CG A:HIS96 4.2 11.6 1.0
CE1 A:HIS91 4.2 11.7 1.0
ND1 A:HIS279 4.3 19.0 1.0
CG A:HIS279 4.4 17.3 1.0
CB A:ASP210 4.5 13.4 1.0
ND1 A:HIS96 4.5 12.0 1.0
CB A:ASP95 4.6 13.5 1.0
ND1 A:HIS93 4.7 14.2 1.0
NE2 A:HIS188 4.8 16.0 1.0
CB A:HIS93 5.0 13.8 1.0

Zinc binding site 2 out of 16 in 6j4n

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Zinc binding site 2 out of 16 in the Structure of Papua New Guinea Mbl-1(Pngm-1) Native


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Papua New Guinea Mbl-1(Pngm-1) Native within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:20.7
occ:1.00
O A:HOH520 2.0 20.3 1.0
ND1 A:HIS93 2.1 14.2 1.0
NE2 A:HIS188 2.1 16.0 1.0
OD2 A:ASP210 2.2 12.9 1.0
NE2 A:HIS91 2.3 10.9 1.0
O A:HOH672 3.0 34.2 1.0
CE1 A:HIS188 3.0 16.7 1.0
CE1 A:HIS93 3.0 14.3 1.0
CD2 A:HIS91 3.0 11.4 1.0
ZN A:ZN401 3.1 25.9 1.0
CD2 A:HIS188 3.2 16.6 1.0
CG A:HIS93 3.2 14.2 1.0
CG A:ASP210 3.3 13.9 1.0
CE1 A:HIS91 3.4 11.7 1.0
CB A:HIS93 3.6 13.8 1.0
CB A:ASP210 3.8 13.4 1.0
ND1 A:HIS188 4.1 16.6 1.0
NE2 A:HIS93 4.1 14.2 1.0
CD2 A:HIS96 4.2 11.1 1.0
CG A:HIS188 4.2 16.1 1.0
CD2 A:HIS93 4.3 14.2 1.0
CG A:HIS91 4.3 11.1 1.0
NE2 A:HIS96 4.3 11.3 1.0
OD1 A:ASP210 4.4 15.8 1.0
ND1 A:HIS91 4.4 11.2 1.0
O A:HOH656 4.4 31.6 1.0
OD2 A:ASP95 4.5 14.3 1.0
O A:HOH650 4.8 35.0 1.0
OD1 A:ASP95 4.8 14.7 1.0

Zinc binding site 3 out of 16 in 6j4n

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Zinc binding site 3 out of 16 in the Structure of Papua New Guinea Mbl-1(Pngm-1) Native


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Papua New Guinea Mbl-1(Pngm-1) Native within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:25.0
occ:1.00
O B:HOH506 2.1 11.7 1.0
OD2 B:ASP210 2.1 13.4 1.0
NE2 B:HIS279 2.2 16.5 1.0
NE2 B:HIS96 2.4 8.2 1.0
OD1 B:ASP95 2.4 14.7 1.0
O B:HOH686 2.8 28.4 1.0
CD2 B:HIS96 2.9 8.6 1.0
CG B:ASP210 3.0 13.4 1.0
CE1 B:HIS279 3.1 18.9 1.0
ZN B:ZN402 3.1 16.4 1.0
CG B:ASP95 3.2 12.5 1.0
OD1 B:ASP210 3.3 15.1 1.0
CD2 B:HIS279 3.3 16.7 1.0
OD2 B:ASP95 3.5 12.5 1.0
CE1 B:HIS96 3.6 9.3 1.0
NE2 B:HIS91 4.0 8.7 1.0
O B:HOH657 4.0 31.4 1.0
O B:HOH560 4.1 19.2 1.0
CG B:HIS96 4.2 8.3 1.0
CE1 B:HIS91 4.2 8.4 1.0
ND1 B:HIS279 4.2 19.2 1.0
CG B:HIS279 4.4 16.6 1.0
CB B:ASP210 4.4 13.0 1.0
ND1 B:HIS96 4.5 9.0 1.0
CB B:ASP95 4.6 12.3 1.0
ND1 B:HIS93 4.9 10.8 1.0
NE2 B:HIS188 4.9 13.6 1.0

Zinc binding site 4 out of 16 in 6j4n

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Zinc binding site 4 out of 16 in the Structure of Papua New Guinea Mbl-1(Pngm-1) Native


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Papua New Guinea Mbl-1(Pngm-1) Native within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:16.4
occ:1.00
O B:HOH506 2.0 11.7 1.0
ND1 B:HIS93 2.2 10.8 1.0
NE2 B:HIS91 2.2 8.7 1.0
NE2 B:HIS188 2.2 13.6 1.0
OD2 B:ASP210 2.3 13.4 1.0
O B:HOH686 2.8 28.4 1.0
CE1 B:HIS93 3.1 10.8 1.0
CD2 B:HIS91 3.1 8.9 1.0
ZN B:ZN401 3.1 25.0 1.0
CE1 B:HIS188 3.1 13.2 1.0
CD2 B:HIS188 3.2 13.2 1.0
CG B:HIS93 3.2 10.9 1.0
CE1 B:HIS91 3.3 8.4 1.0
CG B:ASP210 3.4 13.4 1.0
CB B:HIS93 3.6 11.3 1.0
CB B:ASP210 3.8 13.0 1.0
CD2 B:HIS96 4.1 8.6 1.0
NE2 B:HIS93 4.2 10.4 1.0
ND1 B:HIS188 4.2 12.6 1.0
CG B:HIS91 4.3 8.8 1.0
NE2 B:HIS96 4.3 8.2 1.0
CD2 B:HIS93 4.3 11.3 1.0
ND1 B:HIS91 4.3 8.2 1.0
CG B:HIS188 4.3 13.3 1.0
O B:HOH657 4.4 31.4 1.0
OD2 B:ASP95 4.4 12.5 1.0
OD1 B:ASP210 4.4 15.1 1.0
OD1 B:ASP95 4.8 14.7 1.0

Zinc binding site 5 out of 16 in 6j4n

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Zinc binding site 5 out of 16 in the Structure of Papua New Guinea Mbl-1(Pngm-1) Native


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Papua New Guinea Mbl-1(Pngm-1) Native within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:30.7
occ:1.00
O C:HOH505 2.1 30.3 1.0
OD2 C:ASP210 2.2 16.8 1.0
NE2 C:HIS279 2.3 21.7 1.0
OD1 C:ASP95 2.4 19.5 1.0
NE2 C:HIS96 2.5 12.8 1.0
O C:HOH658 2.9 25.8 1.0
CD2 C:HIS96 3.0 12.8 1.0
ZN C:ZN402 3.0 24.5 1.0
CG C:ASP210 3.0 18.4 1.0
CE1 C:HIS279 3.1 25.2 1.0
CG C:ASP95 3.2 21.4 1.0
OD1 C:ASP210 3.3 19.0 1.0
CD2 C:HIS279 3.4 22.4 1.0
OD2 C:ASP95 3.6 23.0 1.0
CE1 C:HIS96 3.7 13.0 1.0
NE2 C:HIS91 3.9 18.8 1.0
CE1 C:HIS91 4.2 18.9 1.0
CG C:HIS96 4.3 13.3 1.0
ND1 C:HIS279 4.3 24.5 1.0
CB C:ASP210 4.4 18.6 1.0
CG C:HIS279 4.5 21.8 1.0
CB C:ASP95 4.5 19.9 1.0
ND1 C:HIS96 4.6 12.4 1.0
ND1 C:HIS93 4.6 15.3 1.0
NE2 C:HIS188 4.9 23.8 1.0
CB C:HIS93 4.9 16.4 1.0

Zinc binding site 6 out of 16 in 6j4n

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Zinc binding site 6 out of 16 in the Structure of Papua New Guinea Mbl-1(Pngm-1) Native


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Papua New Guinea Mbl-1(Pngm-1) Native within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:24.5
occ:1.00
O C:HOH505 2.0 30.3 1.0
ND1 C:HIS93 2.1 15.3 1.0
OD2 C:ASP210 2.2 16.8 1.0
NE2 C:HIS91 2.2 18.8 1.0
NE2 C:HIS188 2.3 23.8 1.0
O C:HOH658 2.9 25.8 1.0
CE1 C:HIS93 2.9 15.2 1.0
ZN C:ZN401 3.0 30.7 1.0
CD2 C:HIS91 3.0 17.1 1.0
CE1 C:HIS188 3.1 25.7 1.0
CG C:HIS93 3.1 15.5 1.0
CD2 C:HIS188 3.2 23.5 1.0
CG C:ASP210 3.3 18.4 1.0
CE1 C:HIS91 3.3 18.9 1.0
CB C:HIS93 3.5 16.4 1.0
CB C:ASP210 3.8 18.6 1.0
NE2 C:HIS93 4.1 15.7 1.0
CD2 C:HIS96 4.1 12.8 1.0
NE2 C:HIS96 4.2 12.8 1.0
CD2 C:HIS93 4.2 14.7 1.0
ND1 C:HIS188 4.2 23.2 1.0
CG C:HIS91 4.3 18.4 1.0
CG C:HIS188 4.3 21.9 1.0
ND1 C:HIS91 4.4 19.2 1.0
OD1 C:ASP210 4.4 19.0 1.0
OD2 C:ASP95 4.4 23.0 1.0
OD1 C:ASP95 4.7 19.5 1.0
CG C:ASP95 4.9 21.4 1.0
CA C:HIS93 5.0 15.9 1.0
O C:HOH599 5.0 37.4 1.0

Zinc binding site 7 out of 16 in 6j4n

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Zinc binding site 7 out of 16 in the Structure of Papua New Guinea Mbl-1(Pngm-1) Native


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Papua New Guinea Mbl-1(Pngm-1) Native within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:29.7
occ:1.00
O D:HOH508 2.1 21.5 1.0
OD2 D:ASP210 2.1 15.2 1.0
NE2 D:HIS279 2.2 21.5 1.0
NE2 D:HIS96 2.4 12.2 1.0
OD1 D:ASP95 2.5 18.4 1.0
O D:HOH664 2.9 32.6 1.0
CD2 D:HIS96 3.0 13.1 1.0
CG D:ASP210 3.0 16.1 1.0
ZN D:ZN402 3.1 19.8 1.0
CE1 D:HIS279 3.1 22.5 1.0
OD1 D:ASP210 3.2 17.1 1.0
CD2 D:HIS279 3.3 22.0 1.0
CG D:ASP95 3.3 17.9 1.0
OD2 D:ASP95 3.5 18.9 1.0
CE1 D:HIS96 3.7 12.7 1.0
NE2 D:HIS91 3.9 15.8 1.0
O D:HOH670 4.1 30.7 1.0
ND1 D:HIS279 4.2 25.9 1.0
CE1 D:HIS91 4.3 17.5 1.0
CG D:HIS96 4.3 13.1 1.0
CG D:HIS279 4.3 23.0 1.0
CB D:ASP210 4.4 16.0 1.0
ND1 D:HIS96 4.6 11.9 1.0
CB D:ASP95 4.6 17.4 1.0
ND1 D:HIS93 4.7 14.7 1.0
NE2 D:HIS188 4.7 16.0 1.0
CB D:HIS93 4.9 16.0 1.0

Zinc binding site 8 out of 16 in 6j4n

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Zinc binding site 8 out of 16 in the Structure of Papua New Guinea Mbl-1(Pngm-1) Native


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Papua New Guinea Mbl-1(Pngm-1) Native within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:19.8
occ:1.00
ND1 D:HIS93 2.0 14.7 1.0
O D:HOH508 2.1 21.5 1.0
NE2 D:HIS188 2.2 16.0 1.0
OD2 D:ASP210 2.2 15.2 1.0
NE2 D:HIS91 2.3 15.8 1.0
O D:HOH664 2.7 32.6 1.0
CE1 D:HIS93 2.9 15.9 1.0
CD2 D:HIS91 3.0 15.6 1.0
ZN D:ZN401 3.1 29.7 1.0
CD2 D:HIS188 3.1 16.8 1.0
CG D:HIS93 3.1 16.2 1.0
CE1 D:HIS188 3.2 17.8 1.0
CG D:ASP210 3.3 16.1 1.0
CE1 D:HIS91 3.4 17.5 1.0
CB D:HIS93 3.5 16.0 1.0
CB D:ASP210 3.8 16.0 1.0
NE2 D:HIS93 4.1 16.7 1.0
CD2 D:HIS96 4.1 13.1 1.0
CD2 D:HIS93 4.2 17.0 1.0
NE2 D:HIS96 4.2 12.2 1.0
CG D:HIS188 4.2 16.3 1.0
CG D:HIS91 4.2 16.1 1.0
ND1 D:HIS188 4.2 16.7 1.0
OD1 D:ASP210 4.4 17.1 1.0
ND1 D:HIS91 4.4 16.8 1.0
O D:HOH670 4.4 30.7 1.0
OD2 D:ASP95 4.5 18.9 1.0
OD1 D:ASP95 4.9 18.4 1.0
CA D:HIS93 5.0 15.6 1.0

Zinc binding site 9 out of 16 in 6j4n

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Zinc binding site 9 out of 16 in the Structure of Papua New Guinea Mbl-1(Pngm-1) Native


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Papua New Guinea Mbl-1(Pngm-1) Native within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:27.9
occ:1.00
O E:HOH511 2.2 30.6 1.0
NE2 E:HIS279 2.3 18.6 1.0
OD1 E:ASP95 2.3 16.6 1.0
OD2 E:ASP210 2.3 15.3 1.0
NE2 E:HIS96 2.4 12.7 1.0
CD2 E:HIS96 3.0 12.7 1.0
CG E:ASP210 3.1 17.3 1.0
CE1 E:HIS279 3.1 21.0 1.0
OD1 E:ASP210 3.1 16.7 1.0
ZN E:ZN402 3.1 18.9 1.0
O E:HOH660 3.1 33.5 1.0
CG E:ASP95 3.2 17.9 1.0
CD2 E:HIS279 3.4 19.1 1.0
OD2 E:ASP95 3.5 18.5 1.0
CE1 E:HIS96 3.6 13.9 1.0
NE2 E:HIS91 4.1 12.2 1.0
O E:HOH614 4.1 20.1 1.0
CG E:HIS96 4.2 12.6 1.0
O E:HOH658 4.2 25.2 1.0
ND1 E:HIS279 4.3 20.2 1.0
CE1 E:HIS91 4.3 13.0 1.0
CG E:HIS279 4.4 19.3 1.0
ND1 E:HIS96 4.5 13.9 1.0
CB E:ASP210 4.5 16.9 1.0
CB E:ASP95 4.5 16.0 1.0
ND1 E:HIS93 4.7 12.1 1.0
NE2 E:HIS188 4.8 25.1 1.0
O E:HOH607 5.0 32.1 1.0

Zinc binding site 10 out of 16 in 6j4n

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Zinc binding site 10 out of 16 in the Structure of Papua New Guinea Mbl-1(Pngm-1) Native


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Papua New Guinea Mbl-1(Pngm-1) Native within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:18.9
occ:1.00
O E:HOH511 2.0 30.6 1.0
OD2 E:ASP210 2.0 15.3 1.0
ND1 E:HIS93 2.1 12.1 1.0
NE2 E:HIS188 2.2 25.1 1.0
NE2 E:HIS91 2.2 12.2 1.0
O E:HOH660 2.9 33.5 1.0
CE1 E:HIS93 3.0 12.2 1.0
CD2 E:HIS91 3.1 11.8 1.0
CE1 E:HIS188 3.1 23.4 1.0
ZN E:ZN401 3.1 27.9 1.0
CG E:ASP210 3.1 17.3 1.0
CG E:HIS93 3.2 11.1 1.0
CD2 E:HIS188 3.2 22.9 1.0
CE1 E:HIS91 3.3 13.0 1.0
CB E:HIS93 3.6 11.1 1.0
CB E:ASP210 3.8 16.9 1.0
NE2 E:HIS93 4.1 13.0 1.0
OD1 E:ASP210 4.1 16.7 1.0
CD2 E:HIS96 4.2 12.7 1.0
NE2 E:HIS96 4.2 12.7 1.0
ND1 E:HIS188 4.2 23.1 1.0
CD2 E:HIS93 4.2 12.5 1.0
CG E:HIS91 4.3 12.0 1.0
CG E:HIS188 4.3 23.8 1.0
ND1 E:HIS91 4.3 12.1 1.0
OD2 E:ASP95 4.5 18.5 1.0
O E:HOH658 4.6 25.2 1.0
O E:HOH607 4.6 32.1 1.0
OD1 E:ASP95 4.7 16.6 1.0
CG E:ASP95 5.0 17.9 1.0

Reference:

K.S.Park, M.K.Hong, J.W.Jeon, J.H.Kim, J.H.Jeon, J.H.Lee, T.Y.Kim, A.M.Karim, S.K.Malik, L.W.Kang, S.H.Lee. The Novel Metallo-Beta-Lactamase Pngm-1 From A Deep-Sea Sediment Metagenome: Crystallization and X-Ray Crystallographic Analysis. Acta Crystallogr F Struct V. 74 644 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 30279316
DOI: 10.1107/S2053230X18012268
Page generated: Wed Dec 16 12:02:45 2020

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