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Nickel in PDB 2afb: Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution

Protein crystallography data

The structure of Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution, PDB code: 2afb was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.63 / 2.05
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 120.993, 120.993, 260.300, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 23

Other elements in 2afb:

The structure of Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution (pdb code 2afb). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution, PDB code: 2afb:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 2afb

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Nickel binding site 1 out of 6 in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution


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 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni340

b:32.2
occ:1.00
ND1 A:HIS67 2.1 22.7 1.0
O A:HOH346 2.2 9.7 1.0
O B:HOH345 2.3 19.3 1.0
O A:HOH345 2.6 20.5 1.0
CE1 A:HIS67 2.9 21.5 1.0
CG A:HIS67 3.2 25.9 1.0
CB A:HIS67 3.6 25.1 1.0
O A:HOH516 3.9 49.0 1.0
NE2 A:HIS67 4.1 31.8 1.0
CA A:HIS67 4.1 25.7 1.0
O B:HOH446 4.1 38.6 1.0
CD2 A:HIS67 4.2 26.6 1.0
CD A:LYS70 4.5 35.6 1.0
NZ A:LYS70 4.9 42.0 1.0
OG1 A:THR30 4.9 32.7 1.0
CE1 A:PHE71 5.0 28.3 1.0

Nickel binding site 2 out of 6 in 2afb

Go back to Nickel Binding Sites List in 2afb
Nickel binding site 2 out of 6 in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution


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 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni341

b:17.1
occ:0.33
NE2 A:HIS271 2.1 23.1 1.0
O A:HOH347 2.2 15.1 0.3
CE1 A:HIS271 3.0 32.5 1.0
CD2 A:HIS271 3.1 26.1 1.0
ND1 A:HIS271 4.1 22.3 1.0
CG A:HIS271 4.2 28.3 1.0
CG2 A:VAL249 4.7 29.9 1.0

Nickel binding site 3 out of 6 in 2afb

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Nickel binding site 3 out of 6 in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution


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 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni342

b:42.8
occ:1.00
OD2 A:ASP48 2.1 34.1 1.0
ND1 A:HIS0 2.2 48.9 1.0
O A:HOH348 2.4 29.7 1.0
O A:HOH349 2.5 30.2 1.0
CG A:ASP48 2.9 30.1 1.0
CG A:HIS0 3.1 40.9 1.0
OD1 A:ASP48 3.1 23.3 1.0
CB A:HIS0 3.2 33.3 1.0
CE1 A:HIS0 3.3 51.1 1.0
O A:HOH486 3.9 36.9 1.0
CA A:HIS0 3.9 34.9 1.0
CB A:ASP48 4.2 29.5 1.0
CD2 A:HIS0 4.3 47.3 1.0
NE2 A:HIS-2 4.3 58.3 1.0
NE2 A:HIS0 4.3 49.8 1.0
C A:HIS0 4.8 33.4 1.0
CE A:LYS74 4.9 47.3 1.0
CD2 A:HIS-2 5.0 66.9 1.0

Nickel binding site 4 out of 6 in 2afb

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Nickel binding site 4 out of 6 in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni340

b:33.5
occ:1.00
ND1 B:HIS67 2.0 30.1 1.0
O B:HOH347 2.2 10.3 1.0
O B:HOH346 2.3 15.6 1.0
O B:HOH348 2.7 19.6 1.0
CE1 B:HIS67 2.9 26.6 1.0
CG B:HIS67 3.1 30.5 1.0
CB B:HIS67 3.5 27.9 1.0
CA B:HIS67 4.0 25.5 1.0
NE2 B:HIS67 4.0 29.8 1.0
CD2 B:HIS67 4.1 31.2 1.0
CD B:LYS70 4.5 32.0 1.0
O B:HOH501 4.8 33.9 1.0
CE1 B:PHE71 4.9 28.7 1.0
N B:HIS67 4.9 22.3 1.0

Nickel binding site 5 out of 6 in 2afb

Go back to Nickel Binding Sites List in 2afb
Nickel binding site 5 out of 6 in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni341

b:14.1
occ:0.33
NE2 B:HIS271 2.0 23.3 1.0
O B:HOH349 2.3 14.9 0.3
CE1 B:HIS271 3.0 24.6 1.0
CD2 B:HIS271 3.0 20.8 1.0
ND1 B:HIS271 4.1 25.3 1.0
CG B:HIS271 4.2 29.9 1.0
CG2 B:VAL249 4.2 31.6 1.0

Nickel binding site 6 out of 6 in 2afb

Go back to Nickel Binding Sites List in 2afb
Nickel binding site 6 out of 6 in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni342

b:50.3
occ:1.00
O B:HOH350 2.2 31.8 1.0
NE2 B:HIS263 2.2 28.1 1.0
O B:HOH351 2.8 29.6 1.0
CD2 B:HIS263 3.0 20.7 1.0
O B:HOH513 3.2 43.4 1.0
CE1 B:HIS263 3.3 27.4 1.0
CG B:HIS263 4.2 27.6 1.0
CB B:SER296 4.3 29.1 1.0
ND1 B:HIS263 4.3 28.5 1.0
O B:HOH505 4.3 39.1 1.0
O B:HOH493 4.6 48.6 1.0
OG B:SER296 4.6 22.2 1.0
CB B:GLN261 4.8 27.9 1.0

Reference:

I.I.Mathews, D.Mcmullan, M.D.Miller, J.M.Canaves, M.A.Elsliger, R.Floyd, S.K.Grzechnik, L.Jaroszewski, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, T.M.Mcphillips, A.T.Morse, K.Quijano, C.L.Rife, R.Schwarzenbacher, G.Spraggon, R.C.Stevens, H.Van Den Bedem, D.Weekes, G.Wolf, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson. Crystal Structure of 2-Keto-3-Deoxygluconate Kinase (TM0067) From Thermotoga Maritima at 2.05 A Resolution. Proteins V. 70 603 2007.
ISSN: ISSN 0887-3585
PubMed: 18004772
DOI: 10.1002/PROT.21842
Page generated: Thu Oct 29 06:16:32 2020
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