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Manganese in PDB 6iht: Crystal Structure of Bacterial Serine Phosphatase Bound with Phosphorylated Peptide

Enzymatic activity of Crystal Structure of Bacterial Serine Phosphatase Bound with Phosphorylated Peptide

All present enzymatic activity of Crystal Structure of Bacterial Serine Phosphatase Bound with Phosphorylated Peptide:
3.1.3.16;

Protein crystallography data

The structure of Crystal Structure of Bacterial Serine Phosphatase Bound with Phosphorylated Peptide, PDB code: 6iht was solved by C.-G.Yang, T.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.69 / 1.57
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.693, 38.609, 65.003, 90.00, 101.89, 90.00
R / Rfree (%) 15.9 / 18.3

Other elements in 6iht:

The structure of Crystal Structure of Bacterial Serine Phosphatase Bound with Phosphorylated Peptide also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Bacterial Serine Phosphatase Bound with Phosphorylated Peptide (pdb code 6iht). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Bacterial Serine Phosphatase Bound with Phosphorylated Peptide, PDB code: 6iht:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6iht

Go back to Manganese Binding Sites List in 6iht
Manganese binding site 1 out of 4 in the Crystal Structure of Bacterial Serine Phosphatase Bound with Phosphorylated Peptide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Bacterial Serine Phosphatase Bound with Phosphorylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:15.7
occ:1.00
OD1 A:ASP192 2.1 17.5 1.0
OD2 A:ASP231 2.1 16.7 1.0
OD2 A:ASP35 2.2 14.0 1.0
O A:HOH462 2.2 15.7 1.0
O3P X:SEP3 2.2 20.0 1.0
O2P X:SEP3 2.4 16.6 1.0
P X:SEP3 2.8 24.8 0.3
CG A:ASP231 3.1 17.0 1.0
CG A:ASP35 3.1 14.1 1.0
CG A:ASP192 3.1 15.6 1.0
OD1 A:ASP35 3.4 14.3 1.0
OD1 A:ASP231 3.4 18.4 1.0
OD2 A:ASP192 3.6 16.4 1.0
O1P X:SEP3 3.8 17.2 1.0
MN A:MN304 3.8 14.9 0.5
O X:HOH101 3.9 35.4 1.0
OG X:SEP3 4.0 27.4 1.0
N A:GLY193 4.0 14.6 1.0
O A:HOH454 4.1 15.5 1.0
O A:HOH469 4.2 14.2 1.0
O A:HOH411 4.3 26.0 1.0
OD1 A:ASP17 4.4 17.2 1.0
CB A:ASP231 4.4 17.7 1.0
CB A:ASP35 4.4 12.9 1.0
N A:ASP192 4.5 15.5 1.0
CB A:ASP192 4.5 14.4 1.0
O A:HOH428 4.5 15.1 1.0
O A:ASN232 4.5 17.1 1.0
C A:ASP192 4.6 18.1 1.0
CA A:ASP192 4.7 17.3 1.0
CA A:GLY193 4.8 15.2 1.0
CB X:SEP3 4.9 55.5 1.0
CB A:SER191 4.9 15.9 1.0
O X:HOH102 4.9 16.3 1.0
OG A:SER191 4.9 17.0 1.0

Manganese binding site 2 out of 4 in 6iht

Go back to Manganese Binding Sites List in 6iht
Manganese binding site 2 out of 4 in the Crystal Structure of Bacterial Serine Phosphatase Bound with Phosphorylated Peptide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Bacterial Serine Phosphatase Bound with Phosphorylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn304

b:14.9
occ:0.48
O A:GLY36 2.0 14.8 1.0
O A:HOH428 2.1 15.1 1.0
OD1 A:ASP35 2.1 14.3 1.0
O1P X:SEP3 2.1 17.2 1.0
O2P X:SEP3 2.1 16.6 1.0
O A:HOH457 2.1 14.7 1.0
P X:SEP3 2.6 24.8 0.3
CG A:ASP35 3.2 14.1 1.0
C A:GLY36 3.2 14.8 1.0
OG X:SEP3 3.7 27.4 1.0
OD2 A:ASP35 3.8 14.0 1.0
N A:GLY38 3.8 17.2 1.0
O3P X:SEP3 3.8 20.0 1.0
MN A:MN303 3.8 15.7 1.0
N A:GLY36 3.9 13.3 1.0
O X:HOH102 3.9 16.3 1.0
C A:ASP35 4.0 13.3 1.0
OD1 A:ASP17 4.0 17.2 1.0
CA A:GLY36 4.1 12.7 1.0
N A:MET37 4.2 14.6 1.0
CB A:GLU16 4.2 15.7 1.0
CA A:MET37 4.2 15.9 1.0
C A:MET37 4.3 17.9 1.0
O A:HOH462 4.3 15.7 1.0
OD1 A:ASN232 4.3 17.3 1.0
OE1 A:GLU16 4.3 18.6 1.0
O A:ASP35 4.4 13.7 1.0
OD1 A:ASP231 4.4 18.4 1.0
O A:HOH479 4.4 20.6 1.0
CB A:ASP35 4.4 12.9 1.0
CA A:ASP35 4.5 12.3 1.0
CA A:GLY38 4.5 16.7 1.0
NH1 A:ARG12 4.5 23.9 1.0
O A:GLU16 4.7 15.5 1.0
C A:GLU16 4.7 15.1 1.0
CB X:SEP3 4.9 55.5 1.0

Manganese binding site 3 out of 4 in 6iht

Go back to Manganese Binding Sites List in 6iht
Manganese binding site 3 out of 4 in the Crystal Structure of Bacterial Serine Phosphatase Bound with Phosphorylated Peptide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Bacterial Serine Phosphatase Bound with Phosphorylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn305

b:16.6
occ:0.47
OD2 A:ASP118 2.0 16.2 1.0
OD2 A:ASP192 2.1 16.4 1.0
O A:HOH418 2.1 18.0 1.0
O A:HOH452 2.1 18.4 1.0
O A:HOH427 2.1 18.1 1.0
O A:HOH440 2.2 16.5 1.0
CG A:ASP118 3.2 15.3 1.0
CG A:ASP192 3.2 15.6 1.0
CB A:ASP192 3.6 14.4 1.0
O A:HOH454 3.7 15.5 1.0
OD1 A:ASP118 3.8 16.1 1.0
OD2 A:ASP196 3.9 21.5 1.0
O X:HOH101 4.0 35.4 1.0
O A:HOH547 4.2 34.7 1.0
CB A:ASP118 4.3 16.4 1.0
OD1 A:ASP192 4.3 17.5 1.0
O A:ARG159 4.3 22.7 1.0
OD1 A:ASP196 4.3 19.3 1.0
O A:ASN160 4.3 24.0 1.0
O A:HOH419 4.4 17.8 1.0
OD1 A:ASN160 4.4 32.3 1.0
CA A:ASN160 4.5 23.6 1.0
CG A:ASP196 4.6 23.2 1.0
CG2 A:ILE162 4.6 19.9 1.0
O3P X:SEP3 4.7 20.0 1.0
C A:ASN160 4.8 20.8 1.0

Manganese binding site 4 out of 4 in 6iht

Go back to Manganese Binding Sites List in 6iht
Manganese binding site 4 out of 4 in the Crystal Structure of Bacterial Serine Phosphatase Bound with Phosphorylated Peptide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Bacterial Serine Phosphatase Bound with Phosphorylated Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn306

b:27.4
occ:1.00
O A:HOH529 2.0 26.1 1.0
O A:LYS209 2.2 23.0 1.0
O A:LEU207 2.2 26.9 1.0
OH A:TYR186 2.3 25.5 1.0
NE2 A:HIS216 2.3 25.5 1.0
CD2 A:HIS216 3.3 27.0 1.0
CE1 A:HIS216 3.3 28.9 1.0
C A:LEU207 3.4 25.8 1.0
CZ A:TYR186 3.4 24.9 1.0
C A:LYS209 3.4 23.8 1.0
CE2 A:TYR186 3.8 23.9 1.0
N A:LYS209 3.9 26.1 1.0
C A:VAL208 4.0 27.6 1.0
O A:HOH455 4.2 27.7 1.0
CA A:LEU207 4.2 24.8 1.0
N A:VAL208 4.3 25.1 1.0
CA A:LYS209 4.3 31.3 1.0
CA A:VAL208 4.3 25.9 1.0
O A:GLY211 4.3 29.6 1.0
N A:GLU210 4.4 30.1 1.0
ND1 A:HIS216 4.4 24.6 1.0
CA A:GLU210 4.4 29.9 1.0
CG A:HIS216 4.4 22.2 1.0
C A:GLU210 4.4 35.8 1.0
O A:VAL208 4.5 31.1 1.0
CE1 A:TYR186 4.6 24.0 1.0
N A:GLY211 4.6 32.3 1.0
O A:GLU210 4.8 35.4 1.0
O A:LEU206 4.8 25.3 1.0
CB A:LEU207 4.9 21.0 1.0

Reference:

T.Yang, T.Liu, J.Gan, K.Yu, K.Chen, W.Xue, L.Lan, S.Yang, C.G.Yang. Structural Insight Into the Mechanism of Staphylococcus Aureus STP1 Phosphatase. Acs Infect Dis. V. 5 841 2019.
ISSN: ESSN 2373-8227
PubMed: 30868877
DOI: 10.1021/ACSINFECDIS.8B00316
Page generated: Tue Dec 15 04:54:38 2020

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