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Iron in PDB 6hwr: Red Kidney Bean Purple Acid Phosphatase in Complex with Adenosine Divanadate

Enzymatic activity of Red Kidney Bean Purple Acid Phosphatase in Complex with Adenosine Divanadate

All present enzymatic activity of Red Kidney Bean Purple Acid Phosphatase in Complex with Adenosine Divanadate:
3.1.3.2;

Protein crystallography data

The structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Adenosine Divanadate, PDB code: 6hwr was solved by D.Feder, L.R.Gahan, R.P.Mcgeary, L.W.Guddat, G.Schenk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 1.95
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.242, 126.242, 296.877, 90.00, 90.00, 120.00
R / Rfree (%) 16.3 / 19.9

Other elements in 6hwr:

The structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Adenosine Divanadate also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Vanadium (V) 18 atoms
Sodium (Na) 5 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Red Kidney Bean Purple Acid Phosphatase in Complex with Adenosine Divanadate (pdb code 6hwr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Red Kidney Bean Purple Acid Phosphatase in Complex with Adenosine Divanadate, PDB code: 6hwr:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6hwr

Go back to Iron Binding Sites List in 6hwr
Iron binding site 1 out of 4 in the Red Kidney Bean Purple Acid Phosphatase in Complex with Adenosine Divanadate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Red Kidney Bean Purple Acid Phosphatase in Complex with Adenosine Divanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:21.7
occ:0.81
OH C:TYR167 1.9 16.4 1.0
OD2 C:ASP135 2.1 18.6 1.0
O02 C:H1T520 2.2 15.7 0.6
O03 C:H1T520 2.3 22.3 0.6
NE2 C:HIS325 2.3 17.8 1.0
OD2 C:ASP164 2.3 14.2 1.0
V01 C:H1T520 2.9 28.8 0.6
CG C:ASP135 3.0 12.9 1.0
CZ C:TYR167 3.1 15.6 1.0
CE1 C:HIS325 3.3 19.5 1.0
CG C:ASP164 3.3 13.8 1.0
CD2 C:HIS325 3.3 13.5 1.0
CB C:ASP135 3.4 12.4 1.0
ZN C:ZN501 3.5 20.8 0.9
CB C:ASP164 3.6 12.5 1.0
CE2 C:TYR167 3.6 14.0 1.0
O01 C:H1T520 3.8 22.4 0.6
O C:HIS323 4.0 17.7 1.0
O04 C:H1T520 4.1 21.2 0.6
OD1 C:ASP135 4.2 13.5 1.0
CE1 C:TYR167 4.2 14.8 1.0
CD2 C:HIS202 4.3 16.7 1.0
CA C:ASP135 4.3 10.7 1.0
O07 C:H1T520 4.4 31.9 0.6
CA C:HIS323 4.4 14.1 1.0
ND1 C:HIS325 4.4 17.8 1.0
OD1 C:ASP164 4.4 12.9 1.0
CG C:HIS325 4.5 15.3 1.0
CE1 C:HIS286 4.5 12.1 1.0
NE2 C:HIS202 4.6 16.9 1.0
NE2 C:HIS286 4.6 15.7 1.0
C C:HIS323 4.6 15.9 1.0
O05 C:H1T520 4.8 31.2 0.6
N C:HIS323 4.8 12.5 1.0
CB C:ASN364 4.8 14.8 1.0
CD2 C:TYR167 5.0 11.2 1.0

Iron binding site 2 out of 4 in 6hwr

Go back to Iron Binding Sites List in 6hwr
Iron binding site 2 out of 4 in the Red Kidney Bean Purple Acid Phosphatase in Complex with Adenosine Divanadate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Red Kidney Bean Purple Acid Phosphatase in Complex with Adenosine Divanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:21.9
occ:0.80
O03 B:VV6521 1.9 22.9 0.6
OH B:TYR167 2.0 18.4 1.0
OD2 B:ASP135 2.0 14.3 1.0
O02 B:VV6521 2.3 19.2 0.6
OD1 B:ASP164 2.3 15.5 1.0
NE2 B:HIS325 2.4 19.2 1.0
V01 B:VV6521 2.8 29.8 0.6
CG B:ASP135 3.0 17.1 1.0
CZ B:TYR167 3.1 15.2 1.0
CG B:ASP164 3.3 17.2 1.0
CD2 B:HIS325 3.3 17.6 1.0
CB B:ASP135 3.4 13.5 1.0
CE1 B:HIS325 3.5 19.9 1.0
ZN B:ZN501 3.5 23.9 1.0
CB B:ASP164 3.6 15.3 1.0
CE1 B:TYR167 3.6 15.9 1.0
O04 B:VV6521 3.8 23.1 0.6
O07 B:VV6521 4.1 32.5 0.6
O B:HIS323 4.1 16.5 1.0
OD1 B:ASP135 4.1 19.0 1.0
O01 B:VV6521 4.1 26.6 0.6
CD2 B:HIS202 4.2 20.6 1.0
CE2 B:TYR167 4.2 15.1 1.0
CA B:ASP135 4.3 12.2 1.0
OD2 B:ASP164 4.4 14.4 1.0
CA B:HIS323 4.5 16.4 1.0
NE2 B:HIS202 4.5 23.0 1.0
CG B:HIS325 4.5 19.8 1.0
ND1 B:HIS325 4.6 19.2 1.0
CE1 B:HIS286 4.6 13.2 1.0
NE2 B:HIS286 4.6 16.2 1.0
C B:HIS323 4.7 17.3 1.0
CB B:ASN364 4.8 16.0 1.0
N B:HIS323 4.9 14.6 1.0
CD1 B:TYR167 5.0 17.9 1.0

Iron binding site 3 out of 4 in 6hwr

Go back to Iron Binding Sites List in 6hwr
Iron binding site 3 out of 4 in the Red Kidney Bean Purple Acid Phosphatase in Complex with Adenosine Divanadate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Red Kidney Bean Purple Acid Phosphatase in Complex with Adenosine Divanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:19.8
occ:0.78
OH A:TYR167 2.0 16.9 1.0
OD2 A:ASP135 2.0 16.9 1.0
O3 A:H1Q527 2.1 22.5 0.8
OD2 A:ASP164 2.3 16.1 1.0
O2 A:H1Q527 2.3 28.8 0.8
NE2 A:HIS325 2.5 21.4 1.0
V1 A:H1Q527 3.0 35.9 0.8
CG A:ASP135 3.0 13.4 1.0
CZ A:TYR167 3.1 18.3 1.0
CG A:ASP164 3.3 14.7 1.0
CD2 A:HIS325 3.4 18.7 1.0
CB A:ASP135 3.4 11.4 1.0
ZN A:ZN501 3.5 20.8 0.9
CE1 A:HIS325 3.5 22.6 1.0
CB A:ASP164 3.6 13.2 1.0
CE2 A:TYR167 3.6 18.3 1.0
O5 A:H1Q527 3.9 25.5 0.8
O A:HIS323 4.0 14.9 1.0
O4 A:H1Q527 4.1 27.1 0.8
OD1 A:ASP135 4.2 16.4 1.0
CD2 A:HIS202 4.2 20.9 1.0
CE1 A:TYR167 4.2 14.5 1.0
CA A:ASP135 4.4 14.2 1.0
CA A:HIS323 4.4 12.6 1.0
OD1 A:ASP164 4.4 13.5 1.0
CG A:HIS325 4.6 20.4 1.0
CE1 A:HIS286 4.6 12.6 1.0
NE2 A:HIS286 4.6 12.3 1.0
ND1 A:HIS325 4.6 20.8 1.0
NE2 A:HIS202 4.6 17.0 1.0
C A:HIS323 4.6 16.0 1.0
O9 A:H1Q527 4.7 38.2 0.8
N A:HIS323 4.8 14.7 1.0
CB A:ASN364 4.9 12.6 1.0
CD2 A:TYR167 5.0 11.8 1.0
ND1 A:HIS323 5.0 13.0 1.0

Iron binding site 4 out of 4 in 6hwr

Go back to Iron Binding Sites List in 6hwr
Iron binding site 4 out of 4 in the Red Kidney Bean Purple Acid Phosphatase in Complex with Adenosine Divanadate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Red Kidney Bean Purple Acid Phosphatase in Complex with Adenosine Divanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe502

b:23.0
occ:0.78
O12 D:H1W530 1.8 22.1 0.4
OH D:TYR167 1.9 14.0 1.0
OD1 D:ASP135 2.0 18.4 1.0
OD2 D:ASP164 2.4 17.7 1.0
O10 D:H1W530 2.4 20.7 0.4
O10 D:H1W530 2.4 22.4 0.6
NE2 D:HIS325 2.5 19.3 1.0
V01 D:H1W530 2.8 33.2 0.4
CG D:ASP135 3.0 18.3 1.0
O09 D:H1W530 3.1 27.2 0.6
CZ D:TYR167 3.1 15.1 1.0
CD2 D:HIS325 3.3 17.5 1.0
CG D:ASP164 3.3 15.9 1.0
CB D:ASP135 3.3 11.3 1.0
CE1 D:HIS325 3.5 18.4 1.0
ZN D:ZN501 3.6 19.1 0.8
CB D:ASP164 3.6 10.0 1.0
CE2 D:TYR167 3.6 12.8 1.0
V01 D:H1W530 3.7 46.2 0.6
O09 D:H1W530 3.9 20.1 0.4
O D:HIS323 4.1 15.2 1.0
OD2 D:ASP135 4.1 14.1 1.0
O11 D:H1W530 4.2 27.7 0.4
CE1 D:TYR167 4.2 15.1 1.0
O12 D:H1W530 4.2 29.3 0.6
CD2 D:HIS202 4.2 17.4 1.0
CA D:ASP135 4.3 13.8 1.0
OD1 D:ASP164 4.5 14.4 1.0
CA D:HIS323 4.5 13.4 1.0
CG D:HIS325 4.5 18.7 1.0
O15 D:H1W530 4.5 30.5 0.4
CE1 D:HIS286 4.5 10.9 1.0
NE2 D:HIS286 4.5 14.4 1.0
ND1 D:HIS325 4.6 19.7 1.0
NE2 D:HIS202 4.6 16.5 1.0
C D:HIS323 4.7 17.7 1.0
CB D:ASP364 4.8 12.3 1.0
N D:HIS323 4.8 12.2 1.0
O11 D:H1W530 4.9 31.2 0.6

Reference:

D.Feder, L.R.Gahan, R.P.Mcgeary, L.W.Guddat, G.Schenk. The Binding Mode of An Adp Analogue to A Metallohydrolase Mimics the Likely Transition State. Chembiochem V. 20 1536 2019.
ISSN: ESSN 1439-7633
PubMed: 30719821
DOI: 10.1002/CBIC.201900077
Page generated: Sun Dec 13 16:29:19 2020

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