Atomistry » Nickel » PDB 4lto-4ofl » 4mgg
Atomistry »
  Nickel »
    PDB 4lto-4ofl »
      4mgg »

Nickel in PDB 4mgg: Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121

Protein crystallography data

The structure of Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121, PDB code: 4mgg was solved by M.W.Vetting, X.Zhang, S.R.Wasserman, L.L.Morisco, S.Sojitra, J.B.Bonanno, J.A.Gerlt, S.C.Almo, New York Structural Genomics Research Consortium(Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.81 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.313, 154.897, 181.983, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 21.6

Other elements in 4mgg:

The structure of Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 also contains other interesting chemical elements:

Magnesium (Mg) 17 atoms
Chlorine (Cl) 3 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 (pdb code 4mgg). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121, PDB code: 4mgg:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 4mgg

Go back to Nickel Binding Sites List in 4mgg
Nickel binding site 1 out of 3 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni402

b:18.1
occ:1.00
O G:HOH502 2.0 19.7 1.0
O A:HOH501 2.0 9.8 1.0
O A:HOH502 2.0 13.5 1.0
NE2 G:HIS98 2.0 16.6 1.0
NE2 A:HIS98 2.2 14.8 1.0
O G:HOH501 2.2 11.3 1.0
CE1 G:HIS98 3.0 16.4 1.0
CD2 G:HIS98 3.0 16.9 1.0
CE1 A:HIS98 3.1 17.6 1.0
CD2 A:HIS98 3.2 14.0 1.0
HE1 G:HIS98 3.2 19.7 1.0
HD2 G:HIS98 3.2 20.2 1.0
HE1 A:HIS98 3.3 21.1 1.0
HD2 A:HIS98 3.3 16.8 1.0
HG G:SER67 3.7 27.1 1.0
HG A:SER67 3.8 29.1 1.0
OG G:SER67 4.0 22.6 1.0
OG A:SER67 4.1 24.3 1.0
OE2 G:GLU71 4.1 31.5 1.0
ND1 G:HIS98 4.1 16.0 1.0
CG G:HIS98 4.2 15.8 1.0
OE2 A:GLU71 4.2 33.6 1.0
ND1 A:HIS98 4.2 14.4 1.0
HD11 G:LEU95 4.3 20.3 1.0
CG A:HIS98 4.3 14.0 1.0
OE1 G:GLU71 4.4 36.5 1.0
OE1 A:GLU71 4.4 31.2 1.0
O G:HOH533 4.5 21.0 1.0
O G:HOH521 4.5 13.9 1.0
HD11 A:LEU95 4.5 26.3 1.0
HA2 A:GLY64 4.6 17.3 1.0
CD G:GLU71 4.7 24.9 1.0
HA2 G:GLY68 4.7 20.3 1.0
CD A:GLU71 4.7 30.6 1.0
HA2 A:GLY68 4.7 17.2 1.0
HA2 G:GLY64 4.8 26.6 1.0
HD1 G:HIS98 4.9 19.2 1.0

Nickel binding site 2 out of 3 in 4mgg

Go back to Nickel Binding Sites List in 4mgg
Nickel binding site 2 out of 3 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni401

b:29.0
occ:1.00
O E:HOH803 2.1 20.7 1.0
NE2 E:HIS98 2.1 32.3 1.0
O E:HOH802 2.1 22.4 1.0
O C:HOH502 2.2 27.0 1.0
O C:HOH501 2.2 27.7 1.0
NE2 C:HIS98 2.2 28.5 1.0
CE1 E:HIS98 3.0 29.8 1.0
CE1 C:HIS98 3.1 29.8 1.0
HE1 C:HIS98 3.2 35.7 1.0
HE1 E:HIS98 3.2 35.8 1.0
CD2 E:HIS98 3.2 28.4 1.0
CD2 C:HIS98 3.3 23.8 1.0
HD2 E:HIS98 3.4 34.1 1.0
HD2 C:HIS98 3.5 28.6 1.0
OE2 E:GLU71 4.0 57.8 1.0
OE2 C:GLU71 4.1 59.9 1.0
O C:HOH602 4.2 32.7 1.0
O E:HOH881 4.2 29.3 1.0
HG E:SER67 4.2 47.1 1.0
ND1 E:HIS98 4.2 30.5 1.0
ND1 C:HIS98 4.2 26.4 1.0
OG E:SER67 4.3 39.2 1.0
CG E:HIS98 4.3 27.6 1.0
HG C:SER67 4.3 60.3 1.0
CG C:HIS98 4.4 26.9 1.0
HD11 E:LEU95 4.4 56.7 1.0
OE1 E:GLU71 4.5 44.8 1.0
OG C:SER67 4.6 50.2 1.0
HD11 C:LEU95 4.6 44.5 1.0
CD E:GLU71 4.7 50.2 1.0
HA2 E:GLY68 4.8 52.4 1.0
HA2 E:GLY64 4.8 51.1 1.0
HA2 C:GLY68 4.8 30.5 1.0
CD C:GLU71 4.8 59.5 1.0
HD21 E:LEU95 4.9 54.2 1.0
OE1 C:GLU71 4.9 65.4 1.0
HD1 E:HIS98 5.0 36.6 1.0
HD21 C:LEU95 5.0 39.3 1.0
HD1 C:HIS98 5.0 31.7 1.0

Nickel binding site 3 out of 3 in 4mgg

Go back to Nickel Binding Sites List in 4mgg
Nickel binding site 3 out of 3 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni401

b:28.1
occ:1.00
O H:HOH502 1.9 14.0 1.0
O H:HOH503 2.0 22.2 1.0
NE2 D:HIS98 2.0 32.9 1.0
O D:HOH501 2.0 25.8 1.0
NE2 H:HIS98 2.0 28.1 1.0
O H:HOH501 2.1 22.6 1.0
CE1 H:HIS98 2.9 27.6 1.0
CE1 D:HIS98 2.9 27.1 1.0
HE1 H:HIS98 3.0 33.2 1.0
HE1 D:HIS98 3.0 32.5 1.0
CD2 D:HIS98 3.1 30.2 1.0
CD2 H:HIS98 3.1 27.6 1.0
HD2 D:HIS98 3.4 36.2 1.0
HD2 H:HIS98 3.4 33.1 1.0
HG H:SER67 3.7 44.1 1.0
OG H:SER67 3.9 36.8 1.0
OE2 H:GLU71 4.0 45.4 1.0
HG D:SER67 4.0 38.6 1.0
ND1 D:HIS98 4.1 25.9 1.0
ND1 H:HIS98 4.1 26.8 1.0
OG D:SER67 4.1 32.1 1.0
O D:HOH523 4.2 24.2 1.0
CG D:HIS98 4.2 32.9 1.0
CG H:HIS98 4.2 26.8 1.0
OE2 D:GLU71 4.3 47.8 1.0
OE1 D:GLU71 4.3 51.6 1.0
OE1 H:GLU71 4.4 40.2 1.0
O D:HOH565 4.4 34.9 1.0
HD11 H:LEU95 4.4 33.2 1.0
HD11 D:LEU95 4.5 45.1 1.0
CD H:GLU71 4.6 46.4 1.0
HA2 H:GLY68 4.7 34.6 1.0
CD D:GLU71 4.7 48.6 1.0
HA2 H:GLY64 4.8 37.0 1.0
HA2 D:GLY64 4.8 33.9 1.0
HA2 D:GLY68 4.8 39.7 1.0
HD1 H:HIS98 4.8 32.2 1.0
HD1 D:HIS98 4.8 31.1 1.0

Reference:

M.W.Vetting, X.Zhang, S.R.Wasserman, L.L.Morisco, S.Sojitra, J.B.Bonanno, J.A.Gerlt, S.C.Almo, New York Structural Genomics Research Consortium (Nysgrc). Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata Iam 12614 (Target Nysgrc-012903) with Bound Mg, Space Group P212121 To Be Published.
Page generated: Wed Dec 16 01:33:03 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy