Phosphorus in PDB 1a80: Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph

Protein crystallography data

The structure of Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph, PDB code: 1a80 was solved by S.Khurana, D.B.Powers, S.Anderson, M.Blaber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.700, 55.800, 74.700, 90.00, 92.20, 90.00
R / Rfree (%) 19.1 / 28.8

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph (pdb code 1a80). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 3 binding sites of Phosphorus where determined in the Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph, PDB code: 1a80:
Jump to Phosphorus binding site number: 1; 2; 3;

Phosphorus binding site 1 out of 3 in 1a80

Go back to Phosphorus Binding Sites List in 1a80
Phosphorus binding site 1 out of 3 in the Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P300

b:17.8
occ:1.00
PA A:NDP300 0.0 17.8 1.0
O1A A:NDP300 1.5 13.4 1.0
O2A A:NDP300 1.5 13.2 1.0
O5B A:NDP300 1.5 19.0 1.0
O3 A:NDP300 1.5 22.1 1.0
C5B A:NDP300 2.7 21.9 1.0
PN A:NDP300 2.9 15.9 1.0
O5D A:NDP300 3.2 10.4 1.0
O2N A:NDP300 3.5 11.2 1.0
CD A:PRO189 3.7 8.1 1.0
C5D A:NDP300 3.8 13.8 1.0
C4B A:NDP300 3.9 22.4 1.0
O1N A:NDP300 4.0 14.3 1.0
CA A:GLN192 4.0 14.4 1.0
N A:GLN192 4.1 13.2 1.0
CA A:GLY188 4.1 8.1 1.0
N A:LEU190 4.2 14.5 1.0
CB A:LEU190 4.3 13.9 1.0
C A:GLY188 4.4 14.2 1.0
O4B A:NDP300 4.4 25.8 1.0
N A:PRO189 4.4 10.1 1.0
CG A:GLN192 4.4 24.2 1.0
N A:LYS232 4.5 9.5 1.0
CG A:PRO189 4.5 13.9 1.0
CA A:LEU190 4.7 14.1 1.0
N A:GLY188 4.8 6.8 1.0
CG A:LEU190 4.8 17.4 1.0
CB A:GLN192 4.8 14.9 1.0
C A:LEU190 4.8 18.8 1.0
CD1 A:LEU190 4.9 15.8 1.0
O A:HOH352 4.9 20.2 1.0
O A:LYS232 4.9 16.2 1.0
CA A:PRO231 4.9 14.1 1.0

Phosphorus binding site 2 out of 3 in 1a80

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Phosphorus binding site 2 out of 3 in the Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P300

b:15.9
occ:1.00
PN A:NDP300 0.0 15.9 1.0
O2N A:NDP300 1.5 11.2 1.0
O1N A:NDP300 1.5 14.3 1.0
O5D A:NDP300 1.5 10.4 1.0
O3 A:NDP300 1.7 22.1 1.0
C5D A:NDP300 2.5 13.8 1.0
PA A:NDP300 2.9 17.8 1.0
O A:HOH352 3.1 20.2 1.0
O2A A:NDP300 3.4 13.2 1.0
O A:HOH342 3.4 17.4 1.0
C4D A:NDP300 3.5 18.5 1.0
C3D A:NDP300 3.5 17.0 1.0
O5B A:NDP300 3.7 19.0 1.0
O1A A:NDP300 3.7 13.4 1.0
O3D A:NDP300 3.9 16.4 1.0
CG A:GLN192 4.0 24.2 1.0
C5B A:NDP300 4.1 21.9 1.0
CA A:GLY188 4.1 8.1 1.0
NE2 A:GLN192 4.1 21.1 1.0
N A:GLY188 4.2 6.8 1.0
O4D A:NDP300 4.3 19.1 1.0
C6N A:NDP300 4.3 18.3 1.0
CD2 A:PHE22 4.5 15.1 1.0
CB A:LYS232 4.5 10.9 1.0
CD A:GLN192 4.6 34.1 1.0
CD A:PRO189 4.6 8.1 1.0
C2D A:NDP300 4.9 18.4 1.0
CB A:GLN192 4.9 14.9 1.0
CA A:GLN192 5.0 14.4 1.0

Phosphorus binding site 3 out of 3 in 1a80

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Phosphorus binding site 3 out of 3 in the Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P300

b:17.7
occ:1.00
P2B A:NDP300 0.0 17.7 1.0
O2B A:NDP300 1.5 20.6 1.0
O3X A:NDP300 1.5 20.2 1.0
O2X A:NDP300 1.5 12.0 1.0
O1X A:NDP300 1.5 16.1 1.0
C2B A:NDP300 2.5 25.1 1.0
O A:HOH406 3.1 54.8 1.0
OG A:SER233 3.4 31.9 1.0
O A:HOH396 3.4 36.5 1.0
NH1 A:ARG238 3.4 23.6 1.0
C3B A:NDP300 3.5 25.4 1.0
C1B A:NDP300 3.6 23.9 1.0
N A:VAL234 3.7 17.2 1.0
CA A:SER233 3.7 17.6 1.0
O3B A:NDP300 3.8 27.7 1.0
CG2 A:VAL234 3.9 18.9 1.0
CB A:SER233 3.9 22.0 1.0
N9A A:NDP300 4.1 20.2 1.0
NZ A:LYS232 4.2 25.0 1.0
C A:SER233 4.2 20.2 1.0
NE A:ARG235 4.3 64.6 1.0
CZ A:ARG235 4.4 89.5 1.0
CD A:ARG235 4.5 35.7 1.0
CD A:ARG238 4.5 21.3 1.0
O A:LYS232 4.6 16.2 1.0
CZ A:ARG238 4.6 38.5 1.0
NH1 A:ARG235 4.6 80.1 1.0
C8A A:NDP300 4.7 21.4 1.0
C4A A:NDP300 4.7 21.9 1.0
NH2 A:ARG235 4.8 73.4 1.0
CA A:VAL234 4.8 16.5 1.0
O4B A:NDP300 4.8 25.8 1.0
C4B A:NDP300 4.8 22.4 1.0
N A:SER233 4.8 17.4 1.0
N A:ARG235 4.8 19.5 1.0
CG A:ARG235 4.9 23.5 1.0
CB A:VAL234 5.0 19.1 1.0
N3A A:NDP300 5.0 24.3 1.0

Reference:

S.Khurana, D.B.Powers, S.Anderson, M.Blaber. Crystal Structure of 2,5-Diketo-D-Gluconic Acid Reductase A Complexed with Nadph at 2.1-A Resolution. Proc.Natl.Acad.Sci.Usa V. 95 6768 1998.
ISSN: ISSN 0027-8424
PubMed: 9618487
DOI: 10.1073/PNAS.95.12.6768
Page generated: Fri Sep 25 12:25:26 2020

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