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Zinc in PDB 4k1t: Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution

Protein crystallography data

The structure of Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution, PDB code: 4k1t was solved by M.Zdzalik, K.Pustelny, J.Stec-Niemczyk, P.Cichon, A.Czarna, G.Popowicz, M.Drag, B.Wladyka, J.Potempa, A.Dubin, G.Dubin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.91 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.740, 77.760, 95.790, 90.00, 131.81, 90.00
R / Rfree (%) 18.4 / 22.3

Other elements in 4k1t:

The structure of Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution (pdb code 4k1t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution, PDB code: 4k1t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 4k1t

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Zinc binding site 1 out of 10 in the Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:6.7
occ:1.00
 NE2 A:HIS123 2.0 7.7 1.0
OD2 B:ASP180 2.0 7.1 1.0
OE1 A:GLU153 2.1 8.2 1.0
CG B:ASP180 2.8 5.9 1.0
CD A:GLU153 3.0 7.8 1.0
CE1 A:HIS123 3.0 7.5 1.0
CD2 A:HIS123 3.0 6.3 1.0
OD1 B:ASP180 3.0 6.1 1.0
OE2 A:GLU153 3.2 10.0 1.0
O A:HOH434 3.9 12.0 1.0
ND2 B:ASN182 4.0 9.0 1.0
ND1 A:HIS123 4.1 8.9 1.0
CG A:HIS123 4.2 6.8 1.0
CB B:ASP180 4.2 6.3 1.0
CE1 A:HIS151 4.3 6.2 1.0
CG A:PRO122 4.3 5.9 1.0
CG A:GLU153 4.3 7.7 1.0
CB A:PRO122 4.5 5.5 1.0

Zinc binding site 2 out of 10 in 4k1t

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Zinc binding site 2 out of 10 in the Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:19.8
occ:0.80
 OD2 A:ASP77 1.9 21.4 1.0
O A:HOH658 2.1 24.5 1.0
ND1 A:HIS39 2.1 12.4 1.0
O A:HOH657 2.2 23.5 1.0
CG A:ASP77 2.8 14.9 1.0
OD1 A:ASP77 3.0 13.3 1.0
CG A:HIS39 3.1 13.9 1.0
CE1 A:HIS39 3.1 11.7 1.0
CB A:HIS39 3.4 15.7 1.0
N A:HIS39 3.8 13.6 1.0
CB A:ASP77 4.1 12.2 1.0
CD2 A:HIS39 4.2 14.6 1.0
NE2 A:HIS39 4.2 15.5 1.0
CA A:HIS39 4.2 13.6 1.0
O A:HOH487 4.5 28.4 1.0
O A:HOH485 4.7 30.1 1.0
C A:LYS38 4.9 11.8 1.0
CB A:ASN37 5.0 7.6 1.0

Zinc binding site 3 out of 10 in 4k1t

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Zinc binding site 3 out of 10 in the Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:6.6
occ:1.00
 OD2 C:ASP181 1.9 7.6 1.0
OD2 B:ASP181 1.9 8.0 1.0
OD2 A:ASP181 2.0 7.1 1.0
O3 A:SO4304 2.0 8.1 1.0
CG C:ASP181 2.7 7.5 1.0
CG A:ASP181 2.7 7.5 1.0
CG B:ASP181 2.7 7.0 1.0
OD1 A:ASP181 2.8 6.5 1.0
OD1 B:ASP181 2.8 7.5 1.0
OD1 C:ASP181 2.8 6.8 1.0
S A:SO4304 3.5 7.2 1.0
O A:HOH403 3.9 6.7 1.0
O A:HOH416 3.9 6.6 1.0
O A:HOH652 3.9 6.4 1.0
O A:ASP180 4.0 7.1 1.0
O C:ASP180 4.0 6.6 1.0
O B:ASP180 4.0 6.8 1.0
CB C:ASP181 4.2 6.9 1.0
CB A:ASP181 4.2 7.3 1.0
CB B:ASP181 4.2 7.3 1.0
O2 A:SO4304 4.2 7.9 1.0
O1 A:SO4304 4.2 8.2 1.0
O4 A:SO4304 4.2 8.0 1.0
NH2 B:ARG183 4.4 16.6 1.0
O A:HOH433 4.4 14.1 1.0
O B:HOH660 4.4 15.0 1.0
O C:HOH664 4.5 14.6 1.0
C A:ASP180 4.5 6.8 1.0
C C:ASP180 4.5 6.8 1.0
C B:ASP180 4.5 6.2 1.0
N A:ASP181 4.8 7.1 1.0
N B:ASP181 4.9 7.3 1.0
CA A:ASP181 4.9 7.6 1.0
N C:ASP181 4.9 7.5 1.0
CA B:ASP181 4.9 7.7 1.0
CA C:ASP181 4.9 7.0 1.0

Zinc binding site 4 out of 10 in 4k1t

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Zinc binding site 4 out of 10 in the Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:6.1
occ:1.00
 NE2 C:HIS151 2.0 7.5 1.0
O4 A:SO4309 2.1 9.5 1.0
N A:ASP180 2.1 6.7 1.0
OD1 A:ASP180 2.1 7.1 1.0
O A:HOH416 2.2 6.6 1.0
O A:ASP180 2.2 7.1 1.0
CA A:ASP180 2.9 6.3 1.0
C A:ASP180 2.9 6.8 1.0
CD2 C:HIS151 3.0 7.3 1.0
CE1 C:HIS151 3.0 6.2 1.0
CG A:ASP180 3.1 6.3 1.0
S A:SO4309 3.3 14.2 0.5
CB A:ASP180 3.5 6.8 1.0
O3 A:SO4309 3.7 14.8 0.5
O2 A:SO4309 3.8 15.9 0.5
O A:HOH404 4.1 10.1 1.0
CG C:HIS151 4.2 5.7 1.0
ND1 C:HIS151 4.2 6.4 1.0
N A:ASP181 4.2 7.1 1.0
O1 A:SO4304 4.2 8.2 1.0
O A:HOH433 4.2 14.1 1.0
OD2 C:ASP181 4.3 7.6 1.0
OD2 A:ASP180 4.3 6.9 1.0
O1 A:SO4309 4.6 13.1 0.5
O3 A:SO4304 4.6 8.1 1.0
O2 A:SO4304 4.6 7.9 1.0
S A:SO4304 4.7 7.2 1.0
CA A:ASP181 4.9 7.6 1.0
OE2 C:GLU153 5.0 10.8 1.0

Zinc binding site 5 out of 10 in 4k1t

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Zinc binding site 5 out of 10 in the Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:6.2
occ:1.00
 NE2 A:HIS151 2.0 6.8 1.0
O4 B:SO4302 2.0 9.8 1.0
OD1 B:ASP180 2.1 6.1 1.0
N B:ASP180 2.1 5.8 1.0
O A:HOH403 2.2 6.7 1.0
O B:ASP180 2.2 6.8 1.0
CA B:ASP180 2.9 6.3 1.0
C B:ASP180 3.0 6.2 1.0
CD2 A:HIS151 3.0 6.7 1.0
CE1 A:HIS151 3.0 6.2 1.0
CG B:ASP180 3.1 5.9 1.0
S B:SO4302 3.3 15.4 0.5
CB B:ASP180 3.5 6.3 1.0
O2 B:SO4302 3.7 17.2 0.5
O1 B:SO4302 3.8 17.8 0.5
ND1 A:HIS151 4.2 6.3 1.0
O B:HOH660 4.2 15.0 1.0
CG A:HIS151 4.2 6.3 1.0
O A:HOH439 4.2 9.8 1.0
O2 A:SO4304 4.2 7.9 1.0
OD2 A:ASP181 4.2 7.1 1.0
N B:ASP181 4.3 7.3 1.0
OD2 B:ASP180 4.3 7.1 1.0
O3 B:SO4302 4.5 15.4 0.5
O4 A:SO4304 4.6 8.0 1.0
O3 A:SO4304 4.6 8.1 1.0
S A:SO4304 4.7 7.2 1.0
O B:HOH541 5.0 31.4 1.0
OE2 A:GLU153 5.0 10.0 1.0

Zinc binding site 6 out of 10 in 4k1t

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Zinc binding site 6 out of 10 in the Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:6.6
occ:1.00
 NE2 B:HIS123 2.0 6.9 1.0
OD1 C:ASP180 2.0 7.2 1.0
OE1 B:GLU153 2.1 7.5 1.0
CG C:ASP180 2.8 6.4 1.0
CE1 B:HIS123 2.9 7.8 1.0
CD B:GLU153 3.0 8.4 1.0
OD2 C:ASP180 3.0 6.6 1.0
CD2 B:HIS123 3.0 7.1 1.0
OE2 B:GLU153 3.2 10.1 1.0
ND2 C:ASN182 4.0 8.7 1.0
O B:HOH430 4.0 14.0 1.0
ND1 B:HIS123 4.1 8.1 1.0
CB C:ASP180 4.2 6.4 1.0
CG B:HIS123 4.2 7.0 1.0
CE1 B:HIS151 4.2 6.8 1.0
CG B:GLU153 4.3 7.5 1.0
CG B:PRO122 4.4 5.9 1.0
CB B:PRO122 4.5 5.7 1.0
O C:HOH425 5.0 14.8 1.0
NE2 B:HIS151 5.0 7.2 1.0

Zinc binding site 7 out of 10 in 4k1t

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Zinc binding site 7 out of 10 in the Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:16.4
occ:0.70
 OD2 B:ASP77 1.9 18.3 1.0
ND1 B:HIS39 2.1 14.7 1.0
O B:HOH571 2.2 21.9 1.0
O B:HOH593 2.3 26.1 1.0
CG B:ASP77 2.8 13.1 1.0
OD1 B:ASP77 2.9 11.4 1.0
CG B:HIS39 3.0 15.0 1.0
CE1 B:HIS39 3.1 13.0 1.0
CB B:HIS39 3.3 17.2 1.0
N B:HIS39 3.9 12.1 1.0
CB B:ASP77 4.1 11.1 1.0
CD2 B:HIS39 4.2 15.0 1.0
NE2 B:HIS39 4.2 13.8 1.0
CA B:HIS39 4.2 13.6 1.0
O B:HOH576 4.3 40.6 1.0
O B:HOH612 4.4 26.2 1.0
O C:HOH597 4.8 27.9 1.0
CB B:ASN37 4.9 7.3 1.0
O B:HOH635 5.0 38.3 1.0
C B:LYS38 5.0 11.2 1.0

Zinc binding site 8 out of 10 in 4k1t

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Zinc binding site 8 out of 10 in the Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:6.1
occ:1.00
 NE2 B:HIS151 2.1 7.2 1.0
OD2 C:ASP180 2.1 6.6 1.0
O4 C:SO4302 2.1 10.6 1.0
N C:ASP180 2.2 5.5 1.0
O A:HOH652 2.2 6.4 1.0
O C:ASP180 2.2 6.6 1.0
CA C:ASP180 2.9 6.5 1.0
C C:ASP180 2.9 6.8 1.0
CD2 B:HIS151 3.0 7.2 1.0
CE1 B:HIS151 3.1 6.8 1.0
CG C:ASP180 3.1 6.4 1.0
S C:SO4302 3.3 16.1 0.5
CB C:ASP180 3.5 6.4 1.0
O1 C:SO4302 3.7 15.3 0.5
O3 C:SO4302 3.8 19.3 0.5
O C:HOH405 4.2 9.9 1.0
ND1 B:HIS151 4.2 6.9 1.0
N C:ASP181 4.2 7.5 1.0
CG B:HIS151 4.2 6.7 1.0
O C:HOH664 4.2 14.6 1.0
O4 A:SO4304 4.2 8.0 1.0
OD2 B:ASP181 4.3 8.0 1.0
OD1 C:ASP180 4.3 7.2 1.0
O3 A:SO4304 4.5 8.1 1.0
O2 C:SO4302 4.6 14.3 0.5
O1 A:SO4304 4.6 8.2 1.0
S A:SO4304 4.7 7.2 1.0
OE2 B:GLU153 4.9 10.1 1.0
CA C:ASP181 5.0 7.0 1.0

Zinc binding site 9 out of 10 in 4k1t

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Zinc binding site 9 out of 10 in the Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:7.1
occ:1.00
 OD2 A:ASP180 1.9 6.9 1.0
NE2 C:HIS123 2.0 7.2 1.0
OE1 C:GLU153 2.1 8.4 1.0
CG A:ASP180 2.8 6.3 1.0
CD C:GLU153 3.0 8.5 1.0
CE1 C:HIS123 3.0 7.3 1.0
CD2 C:HIS123 3.0 6.6 1.0
OD1 A:ASP180 3.0 7.1 1.0
OE2 C:GLU153 3.1 10.8 1.0
ND2 A:ASN182 4.0 9.2 1.0
O C:HOH420 4.0 12.5 1.0
ND1 C:HIS123 4.1 8.7 1.0
CG C:HIS123 4.2 7.1 1.0
CB A:ASP180 4.2 6.8 1.0
CE1 C:HIS151 4.2 6.2 1.0
CG C:PRO122 4.3 5.8 1.0
CG C:GLU153 4.4 7.6 1.0
CB C:PRO122 4.5 5.8 1.0

Zinc binding site 10 out of 10 in 4k1t

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Zinc binding site 10 out of 10 in the Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Gly-Ser-Splb Protease From Staphylococcus Aureus at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn304

b:13.2
occ:0.50
 OD2 C:ASP77 2.0 17.6 1.0
O C:HOH515 2.0 24.9 1.0
ND1 C:HIS39 2.2 14.2 1.0
O C:HOH670 2.3 31.4 1.0
CG C:ASP77 2.8 12.5 1.0
CG C:HIS39 3.0 13.6 1.0
OD1 C:ASP77 3.0 11.4 1.0
CE1 C:HIS39 3.2 12.7 1.0
CB C:HIS39 3.2 15.1 1.0
N C:HIS39 3.8 11.2 1.0
O C:HOH669 4.0 28.9 1.0
CA C:HIS39 4.1 12.7 1.0
CB C:ASP77 4.2 10.8 1.0
CD2 C:HIS39 4.2 16.3 1.0
NE2 C:HIS39 4.3 13.9 1.0
O C:HOH531 4.3 32.3 1.0
O C:HOH555 4.6 26.1 1.0
O C:HOH617 4.6 29.8 1.0
C C:LYS38 4.9 10.9 1.0
CB C:ASN37 5.0 7.0 1.0

Reference:

K.Pustelny, M.Zdzalik, N.Stach, J.Stec-Niemczyk, P.Cichon, A.Czarna, G.Popowicz, P.Mak, M.Drag, G.S.Salvesen, B.Wladyka, J.Potempa, A.Dubin, G.Dubin. Staphylococcal Splb Serine Protease Utilizes A Novel Molecular Mechanism of Activation. J.Biol.Chem. V. 289 15544 2014.
ISSN: ISSN 0021-9258
PubMed: 24713703
DOI: 10.1074/JBC.M113.507616
Page generated: Sun Oct 27 01:35:47 2024

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