Zinc in PDB 7t1u: Crystal Structure of A Superbinder Src SH2 Domain (Ssrcf) in Complex with A High Affinity Phosphopeptide

Enzymatic activity of Crystal Structure of A Superbinder Src SH2 Domain (Ssrcf) in Complex with A High Affinity Phosphopeptide

All present enzymatic activity of Crystal Structure of A Superbinder Src SH2 Domain (Ssrcf) in Complex with A High Affinity Phosphopeptide:
2.7.10.2;

Protein crystallography data

The structure of Crystal Structure of A Superbinder Src SH2 Domain (Ssrcf) in Complex with A High Affinity Phosphopeptide, PDB code: 7t1u was solved by G.D.Martyn, A.U.Singer, N.Manczyk, G.Veggiani, I.Kurinov, F.Sicheri, S.S.Sidhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.57 / 2.65
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 34.87, 35.89, 53.98, 75.85, 74.77, 61.42
R / Rfree (%) 21.8 / 27

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Superbinder Src SH2 Domain (Ssrcf) in Complex with A High Affinity Phosphopeptide (pdb code 7t1u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Superbinder Src SH2 Domain (Ssrcf) in Complex with A High Affinity Phosphopeptide, PDB code: 7t1u:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7t1u

Go back to Zinc Binding Sites List in 7t1u
Zinc binding site 1 out of 4 in the Crystal Structure of A Superbinder Src SH2 Domain (Ssrcf) in Complex with A High Affinity Phosphopeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Superbinder Src SH2 Domain (Ssrcf) in Complex with A High Affinity Phosphopeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:43.1
occ:1.00
 OD2 A:ASP192 2.0 46.9 1.0
OD1 A:ASP194 2.1 49.9 1.0
OD2 A:ASP194 2.1 48.2 1.0
SG A:CYS240 2.2 65.2 1.0
CG A:ASP194 2.4 49.5 1.0
CG A:ASP192 2.9 47.3 1.0
OD1 A:ASP192 3.1 51.2 1.0
CB A:CYS240 3.5 67.0 1.0
CB A:ASP194 3.8 49.6 1.0
O A:HOH404 4.0 42.9 1.0
CB A:ASP192 4.3 44.3 1.0
CA A:ASP194 4.4 44.1 1.0
N A:ASP194 4.7 39.9 1.0
ND2 A:ASN200 4.8 49.8 1.0
O A:PHE193 4.8 46.3 1.0
CE A:LYS202 4.8 56.8 1.0
CA A:CYS240 4.9 66.4 1.0
C A:PHE193 4.9 46.2 1.0

Zinc binding site 2 out of 4 in 7t1u

Go back to Zinc Binding Sites List in 7t1u
Zinc binding site 2 out of 4 in the Crystal Structure of A Superbinder Src SH2 Domain (Ssrcf) in Complex with A High Affinity Phosphopeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Superbinder Src SH2 Domain (Ssrcf) in Complex with A High Affinity Phosphopeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:40.2
occ:1.00
 OD1 B:ASP194 2.1 48.0 1.0
OD2 B:ASP194 2.1 50.4 1.0
OD2 B:ASP192 2.1 46.6 1.0
OD1 B:ASP192 2.2 51.4 1.0
CG B:ASP194 2.3 49.0 1.0
SG B:CYS240 2.4 62.8 1.0
CG B:ASP192 2.5 48.8 1.0
CB B:CYS240 3.7 60.2 1.0
CB B:ASP194 3.8 48.8 1.0
CB B:ASP192 4.0 48.5 1.0
CA B:ASP194 4.3 44.0 1.0
N B:ASP194 4.5 42.5 1.0
O B:PHE193 4.7 45.2 1.0
C B:PHE193 4.7 46.5 1.0
CE B:LYS202 4.9 51.6 1.0

Zinc binding site 3 out of 4 in 7t1u

Go back to Zinc Binding Sites List in 7t1u
Zinc binding site 3 out of 4 in the Crystal Structure of A Superbinder Src SH2 Domain (Ssrcf) in Complex with A High Affinity Phosphopeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Superbinder Src SH2 Domain (Ssrcf) in Complex with A High Affinity Phosphopeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:64.2
occ:1.00
 NE2 B:HIS241 2.0 60.2 1.0
CE1 B:HIS241 2.7 58.6 1.0
CD2 B:HIS241 3.1 59.8 1.0
ND1 B:HIS241 3.8 57.0 1.0
CG B:HIS241 4.1 57.8 1.0
CD B:ARG172 4.4 49.2 0.6
CB B:ARG172 4.6 56.0 0.4
CD B:ARG172 4.6 49.6 0.4
CB B:ARG172 4.6 56.1 0.6
NH1 B:ARG172 4.6 57.3 0.6
CG B:ARG172 5.0 52.2 0.6

Zinc binding site 4 out of 4 in 7t1u

Go back to Zinc Binding Sites List in 7t1u
Zinc binding site 4 out of 4 in the Crystal Structure of A Superbinder Src SH2 Domain (Ssrcf) in Complex with A High Affinity Phosphopeptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Superbinder Src SH2 Domain (Ssrcf) in Complex with A High Affinity Phosphopeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn101

b:70.5
occ:1.00
 OE1 E:GLU3 2.0 100.7 1.0
OE2 E:GLU3 2.0 101.3 1.0
CD E:GLU3 2.2 96.6 1.0
O E:HOH204 2.3 59.2 1.0
O E:HOH202 2.3 53.1 1.0
CG E:GLU3 3.7 86.2 1.0
CB E:GLU3 4.7 82.5 1.0

Reference:

G.D.Martyn, G.Veggiani, U.Kusebauch, S.R.Morrone, B.P.Yates, A.U.Singer, J.Tong, N.Manczyk, G.Gish, Z.Sun, I.Kurinov, F.Sicheri, M.F.Moran, R.L.Moritz, S.S.Sidhu. Engineered SH2 Domains For Targeted Phosphoproteomics. Acs Chem.Biol. V. 17 1472 2022.
ISSN: ESSN 1554-8937
PubMed: 35613471
DOI: 10.1021/ACSCHEMBIO.2C00051
Page generated: Wed Oct 30 11:24:30 2024

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